Variant report

Variant	rs2516474
Chromosome Location	chr6:31503426-31503427
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31496675-31504805	K562	blood:	n/a	n/a
2	POLR2A	chr6:31499380-31504726	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31503287-31503979	GM12891	blood:	n/a	n/a
4	PML	chr6:31503239-31503964	K562	blood:	n/a	n/a
5	POLR2A	chr6:31503402-31503548	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:31503404-31503563	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:31499214-31503706	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:31499387-31504628	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:31503277-31503597	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:31503191-31503927	GM12891	blood:	n/a	n/a
11	POLR2A	chr6:31499310-31504797	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:31503299-31503623	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:31499446-31503904	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:31499455-31504043	K562	blood:	n/a	n/a
15	HEY1	chr6:31503168-31504069	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:31498116-31504635	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:31496067-31504034	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:31496071-31504008	K562	blood:	n/a	n/a
19	POLR2A	chr6:31502376-31504733	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:31495656-31505050	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr6:31496688-31504446	K562	blood:	n/a	n/a
22	POLR2A	chr6:31496018-31504683	HepG2	liver:	n/a	n/a
23	HEY1	chr6:31502359-31504457	K562	blood:	n/a	n/a
24	POLR2A	chr6:31496124-31504583	K562	blood:	n/a	n/a
25	POLR2A	chr6:31502996-31503721	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:31496050-31504648	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr6:31503005-31503592	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:31495793-31504868	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:31498307-31504315	K562	blood:	n/a	n/a
30	POLR2A	chr6:31498116-31504095	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31502088..31504001-chr6:31743213..31745224,2	MCF-7	breast:

No data

Variant related genes	Relation type
DDX39B	TF binding region
ENSG00000204396	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs17207190	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381344	0.83[AMR][1000 genomes]
rs28732141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732142	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732143	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732144	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732145	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28732153	0.83[AMR][1000 genomes]
rs28732155	0.83[AMR][1000 genomes]
rs28732156	0.83[AMR][1000 genomes]
rs28732159	0.83[AMR][1000 genomes]
rs28895015	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905741	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3021366	1.00[ASN][1000 genomes]
rs3093661	0.93[EUR][1000 genomes]
rs3093668	0.95[EUR][1000 genomes]
rs3093726	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093727	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828917	0.88[EUR][1000 genomes]
rs41293856	0.88[EUR][1000 genomes]
rs41293860	0.88[EUR][1000 genomes]
rs41293879	0.88[EUR][1000 genomes]
rs41293887	0.93[EUR][1000 genomes]
rs41293891	0.88[EUR][1000 genomes]
rs41293895	0.98[EUR][1000 genomes]
rs41293899	0.98[EUR][1000 genomes]
rs41293907	0.98[EUR][1000 genomes]
rs41293911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41293919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41315808	0.83[AMR][1000 genomes]
rs4947326	0.81[EUR][1000 genomes]
rs4947327	0.81[EUR][1000 genomes]
rs4959077	0.93[EUR][1000 genomes]
rs4959078	0.98[EUR][1000 genomes]
rs7757162	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757383	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9267497	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
19	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2516474	MICA///MICB	N/A	lymphoblastoid	RTeQTL
rs2516474	MICB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31467400-31506600	Weak transcription	Right Atrium	heart
2	chr6:31495800-31506200	Strong transcription	Thymus	Thymus
3	chr6:31496000-31506200	Strong transcription	Fetal Brain Female	brain
4	chr6:31496200-31506400	Strong transcription	Fetal Stomach	stomach
5	chr6:31496200-31506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:31496400-31505600	Strong transcription	Fetal Thymus	thymus
7	chr6:31496400-31506000	Strong transcription	Brain Germinal Matrix	brain
8	chr6:31496800-31505800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr6:31496800-31506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:31496800-31506400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:31496800-31506400	Strong transcription	Gastric	stomach
12	chr6:31496800-31506600	Strong transcription	Brain Cingulate Gyrus	brain
13	chr6:31496800-31507800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:31497000-31506200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:31497000-31506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:31497000-31506400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:31497200-31503800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:31497200-31504800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:31497200-31505200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:31497200-31505600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:31497200-31506000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:31497200-31506000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:31497200-31506000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:31497200-31506000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:31497200-31506400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:31497200-31506600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:31497200-31506600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:31497200-31506600	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr6:31497200-31506600	Strong transcription	A549	lung
30	chr6:31497200-31506600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:31497200-31506800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr6:31497400-31503600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:31497400-31503800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:31497400-31504000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:31497400-31504800	Strong transcription	Brain Hippocampus Middle	brain
36	chr6:31497400-31505000	Strong transcription	Ovary	ovary
37	chr6:31497400-31505800	Strong transcription	Primary T cells from cord blood	blood
38	chr6:31497400-31506000	Strong transcription	Brain Anterior Caudate	brain
39	chr6:31497400-31506000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:31497400-31506200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:31497400-31506200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:31497400-31506200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr6:31497400-31506200	Strong transcription	Colon Smooth Muscle	Colon
44	chr6:31497400-31506200	Strong transcription	HUVEC	blood vessel
45	chr6:31497400-31506200	Strong transcription	NH-A	brain
46	chr6:31497400-31506200	Strong transcription	NHEK	skin
47	chr6:31497400-31506400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr6:31497400-31506400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:31497400-31506400	Strong transcription	Adipose Nuclei	Adipose
50	chr6:31497400-31506400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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