Variant report

Variant	rs41293899
Chromosome Location	chr6:31481753-31481754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31481733-31481770	MCF-7	breast:	n/a	n/a
2	MYC	chr6:31481686-31481808	MCF-7	breast:	n/a	n/a
3	MYC	chr6:31481706-31481755	MCF-7	breast:	n/a	n/a
4	POLR2A	chr6:31481400-31481777	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr6:31481632-31481763	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31477608..31482305-chr6:31507294..31511382,6	MCF-7	breast:
2	chr6:31479655..31481792-chr6:31482247..31485242,2	K562	blood:
3	chr6:31480216..31481923-chr6:31482906..31485478,2	K562	blood:
4	chr6:31481246..31483555-chr6:31507219..31509095,2	MCF-7	breast:
5	chr6:31472617..31475122-chr6:31479324..31482046,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256851	TF binding region
ENSG00000256851	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000265236	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17207190	0.90[EUR][1000 genomes]
rs2516474	0.98[EUR][1000 genomes]
rs2734576	1.00[ASN][1000 genomes]
rs28732141	0.93[EUR][1000 genomes]
rs28732142	0.93[EUR][1000 genomes]
rs28732143	0.93[EUR][1000 genomes]
rs28732144	0.90[EUR][1000 genomes]
rs28732145	0.85[EUR][1000 genomes]
rs28895015	0.85[EUR][1000 genomes]
rs3093661	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3093662	0.94[ASN][1000 genomes]
rs3093664	0.94[ASN][1000 genomes]
rs3093668	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3093726	0.93[EUR][1000 genomes]
rs3093727	0.93[EUR][1000 genomes]
rs361525	0.94[ASN][1000 genomes]
rs3828917	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41293856	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41293860	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41293879	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293887	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293891	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293895	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293911	0.98[EUR][1000 genomes]
rs41293915	0.98[EUR][1000 genomes]
rs41293919	0.98[EUR][1000 genomes]
rs41293923	0.98[EUR][1000 genomes]
rs4947324	0.84[ASN][1000 genomes]
rs4947326	1.00[ASN][1000 genomes]
rs4947327	1.00[ASN][1000 genomes]
rs4959077	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959078	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959079	1.00[ASN][1000 genomes]
rs7757162	0.95[EUR][1000 genomes]
rs7757383	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9267454	1.00[ASN][1000 genomes]
rs9267456	1.00[ASN][1000 genomes]
rs9267462	1.00[ASN][1000 genomes]
rs9267463	1.00[ASN][1000 genomes]
rs9267464	1.00[ASN][1000 genomes]
rs9267465	1.00[ASN][1000 genomes]
rs9267466	1.00[ASN][1000 genomes]
rs9267487	1.00[ASN][1000 genomes]
rs9267492	1.00[ASN][1000 genomes]
rs9267497	1.00[ASN][1000 genomes]
rs9267502	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
4	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
5	esv3381377	chr6:31192213-31498578	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
6	esv3340592	chr6:31192248-31498535	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
7	nsv1021052	chr6:31206639-31485736	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv1022451	chr6:31279535-31485736	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
10	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
11	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
12	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
13	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
14	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
15	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
16	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
17	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
18	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
19	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
20	esv2752115	chr6:31352880-31498721	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
22	esv2752119	chr6:31359621-31498521	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
23	nsv1022499	chr6:31360095-31485174	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
24	nsv432874	chr6:31379821-31498521	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
25	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
26	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
27	nsv1025961	chr6:31448533-31497835	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
28	nsv1021578	chr6:31448533-31498737	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
29	nsv884414	chr6:31458633-31498497	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
30	nsv884415	chr6:31458633-31501413	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41293899	MICA///MICB	N/A	lymphoblastoid	RTeQTL
rs41293899	MICB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31467400-31506600	Weak transcription	Right Atrium	heart
2	chr6:31474000-31481800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:31475800-31482800	Weak transcription	Right Ventricle	heart
4	chr6:31475800-31493600	Weak transcription	Gastric	stomach
5	chr6:31476000-31482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:31476400-31482200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:31477000-31483400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:31478000-31482600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:31478000-31483400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:31478200-31483800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:31478200-31485000	Weak transcription	K562	blood
12	chr6:31478200-31485600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:31478200-31486400	Weak transcription	HMEC	breast
14	chr6:31478200-31497200	Weak transcription	A549	lung
15	chr6:31478400-31482200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:31478400-31497200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:31478400-31497800	Weak transcription	Primary B cells from cord blood	blood
18	chr6:31478400-31498200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:31478600-31484200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:31478600-31498200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:31479200-31483200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:31479200-31497400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:31479200-31497400	Weak transcription	Primary T cells from cord blood	blood
24	chr6:31479200-31497600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:31479400-31481800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:31479400-31481800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:31479400-31482200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:31479400-31482200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:31479400-31482200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:31479400-31482400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:31479400-31482600	Weak transcription	Dnd41	blood
32	chr6:31479400-31482800	Weak transcription	Adipose Nuclei	Adipose
33	chr6:31479400-31482800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:31479400-31483000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:31479400-31483200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:31479400-31483400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:31479400-31483800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:31479400-31484200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:31479400-31495800	Weak transcription	Thymus	Thymus
40	chr6:31479400-31496400	Weak transcription	Fetal Thymus	thymus
41	chr6:31479400-31497000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:31479400-31497200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:31479400-31497400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:31479400-31497400	Weak transcription	Spleen	Spleen
45	chr6:31479600-31497600	Weak transcription	GM12878-XiMat	blood
46	chr6:31479800-31483400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr6:31479800-31483400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:31480600-31482200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:31480800-31481800	Enhancers	NHLF	lung
50	chr6:31480800-31481800	Enhancers	Osteobl	bone

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