Variant report

Variant	rs10244498
Chromosome Location	chr7:66116056-66116057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:66115978-66116152	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:66115792-66116350	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:66115815-66116255	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr7:66115813-66117293	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66115224..66117671-chr7:66117992..66120004,2	K562	blood:
2	chr7:66057089..66058906-chr7:66114378..66117373,2	MCF-7	breast:
3	chr7:66107277..66110029-chr7:66113989..66116084,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226824	TF binding region
ENSG00000226824	Chromatin interaction
ENSG00000232559	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10107	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs1016265	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10233806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274883	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10278014	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs10281499	0.83[CHB][hapmap];0.94[YRI][hapmap]
rs10950049	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11761542	0.88[CEU][hapmap];0.94[YRI][hapmap]
rs11772819	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12333370	0.84[AFR][1000 genomes]
rs12532998	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap]
rs12673450	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs12698520	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap]
rs13226966	0.82[AFR][1000 genomes]
rs13242290	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13308803	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs13536	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs1544549	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1860469	0.92[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs1860472	0.87[AFR][1000 genomes]
rs1962050	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2003300	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013908	0.89[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2024192	0.81[AFR][1000 genomes]
rs2042133	0.80[EUR][1000 genomes]
rs2109297	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2161065	0.80[EUR][1000 genomes]
rs2420820	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659890	0.84[AFR][1000 genomes]
rs2659891	0.86[AFR][1000 genomes]
rs2659892	0.83[CEU][hapmap];0.87[AFR][1000 genomes]
rs2659893	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs2659894	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659895	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659897	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659898	0.87[AFR][1000 genomes]
rs2659900	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659901	0.85[AFR][1000 genomes]
rs2659904	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659907	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659908	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2659914	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707824	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs2707837	0.85[AFR][1000 genomes]
rs2707839	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2707847	0.87[AFR][1000 genomes]
rs28480509	0.88[AFR][1000 genomes]
rs35149210	0.80[EUR][1000 genomes]
rs3735148	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap]
rs3764903	0.80[MKK][hapmap]
rs3846973	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3857687	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3926380	0.84[AFR][1000 genomes]
rs4506088	0.83[AFR][1000 genomes]
rs4610622	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4717315	0.81[AFR][1000 genomes]
rs4718357	0.80[EUR][1000 genomes]
rs4718383	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58347342	0.85[AFR][1000 genomes]
rs6460302	0.89[CEU][hapmap];0.88[YRI][hapmap]
rs6460304	0.89[CEU][hapmap];0.88[YRI][hapmap]
rs6460307	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs66981195	0.87[AFR][1000 genomes]
rs6945019	1.00[CEU][hapmap]
rs6945032	1.00[CEU][hapmap]
rs6950137	0.89[CEU][hapmap];0.94[YRI][hapmap]
rs6951302	0.86[CEU][hapmap];0.80[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6955837	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs6957199	0.81[EUR][1000 genomes]
rs6958200	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958271	0.80[EUR][1000 genomes]
rs6969679	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6970860	0.81[EUR][1000 genomes]
rs6975044	0.81[AFR][1000 genomes]
rs6978178	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs721717	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7782587	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7789768	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs7792762	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7800620	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs7808013	0.82[AFR][1000 genomes]
rs801195	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs801204	0.92[CEU][hapmap];0.83[CHB][hapmap];0.92[YRI][hapmap]
rs881285	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs974239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9791712	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9791713	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv2761151	chr7:66095738-66138285	Flanking Active TSS Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3496297	chr7:66099491-66136579	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv3496298	chr7:66099491-66136579	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv3486481	chr7:66101377-66137773	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3486482	chr7:66101377-66137773	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv3509629	chr7:66101713-66137585	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv3509631	chr7:66101713-66137585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv967445	chr7:66112743-66133589	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10244498	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs10244498	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs10244498	VKORC1L1	cis	multi-tissue	Pritchard
rs10244498	GS1-124K5.4	cis	Stomach	GTEx
rs10244498	GS1-124K5.4	cis	Artery Aorta	GTEx
rs10244498	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs10244498	TPST1	cis	multi-tissue	Pritchard
rs10244498	RP4-756H11.3	cis	Artery Tibial	GTEx
rs10244498	RP4-756H11.3	cis	lung	GTEx
rs10244498	RP4-756H11.3	cis	Thyroid	GTEx
rs10244498	RP4-756H11.3	cis	Artery Aorta	GTEx
rs10244498	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs10244498	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10244498	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs10244498	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs10244498	GS1-124K5.11	cis	Thyroid	GTEx
rs10244498	LOC285908	cis	multi-tissue	Pritchard
rs10244498	GTF2IRD1P1	cis	Thyroid	GTEx
rs10244498	RNU6-96P	cis	Thyroid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66095200-66118400	Weak transcription	Fetal Heart	heart
2	chr7:66095200-66118400	Weak transcription	HUVEC	blood vessel
3	chr7:66097800-66118200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:66104000-66117600	Weak transcription	Hela-S3	cervix
5	chr7:66104600-66118400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:66104800-66118200	Weak transcription	Pancreas	Pancrea
7	chr7:66104800-66118400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:66105000-66118600	Weak transcription	Esophagus	oesophagus
9	chr7:66105000-66119000	Weak transcription	Gastric	stomach
10	chr7:66105200-66118800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66105600-66118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:66105800-66118400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:66105800-66118400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:66106000-66118200	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:66106000-66118400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:66106600-66118400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:66106800-66118200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:66106800-66118600	Weak transcription	Fetal Kidney	kidney
19	chr7:66107000-66118400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:66107200-66118200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:66107200-66118200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:66107400-66118600	Weak transcription	Fetal Lung	lung
23	chr7:66108000-66118400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:66108600-66118400	Weak transcription	Colonic Mucosa	Colon
25	chr7:66108800-66118200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:66109000-66118000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:66109000-66118000	Weak transcription	Dnd41	blood
28	chr7:66109000-66118000	Weak transcription	K562	blood
29	chr7:66109000-66118200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:66109000-66118200	Weak transcription	A549	lung
31	chr7:66109000-66118200	Weak transcription	HepG2	liver
32	chr7:66109000-66118400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:66109400-66118000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:66109400-66118200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:66109400-66118200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:66109400-66118400	Weak transcription	Fetal Thymus	thymus
37	chr7:66110000-66118200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr7:66110000-66118400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:66110000-66118400	Weak transcription	Psoas Muscle	Psoas
40	chr7:66110000-66118400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:66110000-66118400	Weak transcription	NH-A	brain
42	chr7:66110000-66118800	Weak transcription	Ovary	ovary
43	chr7:66110400-66118200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:66110400-66118200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr7:66110400-66118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:66110400-66118400	Weak transcription	NHLF	lung
47	chr7:66110800-66118400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr7:66110800-66118400	Weak transcription	Liver	Liver
49	chr7:66111000-66118200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr7:66111200-66118200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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