Variant report

Variant	rs2074508
Chromosome Location	chr6:30876438-30876439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:30875380-30876608	IMR90	lung:	n/a	n/a
2	TEAD4	chr6:30875365-30876526	K562	blood:	n/a	n/a
3	NR2F2	chr6:30875067-30876554	K562	blood:	n/a	n/a
4	HCFC1	chr6:30874943-30876583	Hela-S3	cervix:	n/a	n/a
5	PML	chr6:30875462-30876501	K562	blood:	n/a	n/a
6	MTA3	chr6:30875488-30876667	GM12878	blood:	n/a	n/a
7	MXI1	chr6:30875389-30876646	SK-N-SH	brain:	n/a	n/a
8	SIN3A	chr6:30875568-30876438	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:30875342-30876442	K562	blood:	n/a	n/a
10	MAX	chr6:30875379-30876493	K562	blood:	n/a	n/a
11	CREB1	chr6:30875478-30876492	HepG2	liver:	n/a	n/a
12	JUN	chr6:30874741-30876898	K562	blood:	n/a	chr6:30875712-30875721
13	ELF1	chr6:30875510-30876473	K562	blood:	n/a	n/a
14	CTCF	chr6:30876340-30876490	GM12864	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30796384..30798794-chr6:30876100..30879027,2	MCF-7	breast:
2	chr6:30849687..30852078-chr6:30875212..30877587,2	K562	blood:
3	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
4	chr6:30710715..30713404-chr6:30876430..30878574,2	K562	blood:
5	chr6:30856696..30860777-chr6:30873663..30877180,4	K562	blood:
6	chr6:30849765..30853673-chr6:30873635..30876591,7	MCF-7	breast:
7	chr6:30850512..30853465-chr6:30873614..30877587,4	K562	blood:
8	chr6:30687770..30690244-chr6:30875447..30877174,2	MCF-7	breast:
9	chr6:30848838..30854096-chr6:30874501..30878794,8	MCF-7	breast:
10	chr6:30862733..30867301-chr6:30870947..30877299,8	K562	blood:
11	chr6:30855370..30857666-chr6:30876080..30878565,2	MCF-7	breast:
12	chr6:30853891..30856446-chr6:30875282..30877202,3	K562	blood:
13	chr6:30521879..30524871-chr6:30874411..30877273,3	K562	blood:
14	chr6:30861872..30865234-chr6:30873633..30877003,5	MCF-7	breast:
15	chr6:30859072..30860642-chr6:30873697..30876648,2	MCF-7	breast:

No data

Variant related genes	Relation type
GTF2H4	TF binding region
ENSG00000214894	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204576	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1049622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1049628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1052693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215246	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215409	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239518	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285319	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286655	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2524236	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2894055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213644	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3218802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3218815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3909130	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41288539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4618569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711249	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713402	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6457282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6901464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920760	0.82[EUR][1000 genomes]
rs6921687	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6924600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756521	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295929	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9295934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357102	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366761	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368646	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378191	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380200	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468842	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468847	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9501032	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9501035	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9501342	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2074508	VARS2	cis	lymphoblastoid	seeQTL
rs2074508	HIST1H2BJ	cis	parietal	SCAN
rs2074508	ZKSCAN4	cis	cerebellum	SCAN
rs2074508	DDR1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30875000-30876600	Active TSS	GM12878-XiMat	blood
2	chr6:30875000-30877000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:30875200-30876600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:30875200-30876600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:30875200-30876600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:30875200-30876600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:30875200-30876600	Active TSS	Pancreas	Pancrea
8	chr6:30875200-30876600	Active TSS	A549	lung
9	chr6:30875200-30877000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:30875200-30877000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:30875200-30877200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:30875200-30877200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:30875400-30876600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:30875400-30876600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:30875400-30876600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:30875400-30876600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:30875400-30876600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:30875400-30876600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr6:30875400-30876600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:30875400-30876600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr6:30875400-30876600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:30875400-30876600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:30875400-30876600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:30875400-30876600	Active TSS	Brain Germinal Matrix	brain
25	chr6:30875400-30876600	Active TSS	Esophagus	oesophagus
26	chr6:30875400-30876600	Active TSS	Fetal Brain Female	brain
27	chr6:30875400-30876600	Active TSS	Left Ventricle	heart
28	chr6:30875400-30876600	Active TSS	Lung	lung
29	chr6:30875400-30876600	Active TSS	Ovary	ovary
30	chr6:30875400-30876600	Active TSS	Right Ventricle	heart
31	chr6:30875400-30876600	Active TSS	HMEC	breast
32	chr6:30875400-30876600	Active TSS	HSMM	muscle
33	chr6:30875400-30876600	Active TSS	NH-A	brain
34	chr6:30875400-30876600	Active TSS	NHLF	lung
35	chr6:30875400-30876800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:30875400-30876800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:30875400-30876800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr6:30875400-30876800	Active TSS	Psoas Muscle	Psoas
39	chr6:30875400-30877000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr6:30875400-30877000	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:30875400-30877000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:30875400-30877000	Active TSS	Aorta	Aorta
43	chr6:30875600-30876600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30875600-30876600	Active TSS	Fetal Stomach	stomach
45	chr6:30875600-30876600	Active TSS	NHDF-Ad	bronchial
46	chr6:30875600-30876800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr6:30875600-30877000	Active TSS	HSMMtube	muscle
48	chr6:30876000-30876600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:30876000-30876600	Active TSS	Placenta Amnion	Placenta Amnion
50	chr6:30876000-30876600	Bivalent/Poised TSS	HepG2	liver

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