Variant report

Variant	rs10250907
Chromosome Location	chr7:120992731-120992732
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	BATF	chr7:120992468-120992816	GM12878	blood:	n/a	chr7:120992622-120992631
2	BATF	chr7:120992497-120992736	GM12878	blood:	n/a	chr7:120992622-120992631
3	POLR2A	chr7:120992223-120993008	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:120992675-120994097	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120982229..120984096-chr7:120992298..120995156,2	K562	blood:
2	chr7:120991795..120993845-chr7:121034927..121036634,2	MCF-7	breast:

Variant related genes	Relation type
FAM3C	TF binding region
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10250624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762263	0.91[EUR][1000 genomes]
rs11762452	0.85[EUR][1000 genomes]
rs11768996	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770098	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771477	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706337	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706338	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706339	0.85[EUR][1000 genomes]
rs12706340	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706341	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706342	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238085	0.85[EUR][1000 genomes]
rs17143305	0.85[EUR][1000 genomes]
rs1803389	0.89[EUR][1000 genomes]
rs1990447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041490	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240982	1.00[ASN][1000 genomes]
rs2254591	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536155	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536158	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2536159	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536173	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536176	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536184	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536188	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2536190	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2536191	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707460	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707461	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707462	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2707463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707467	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707468	0.85[EUR][1000 genomes]
rs2707470	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707471	0.85[EUR][1000 genomes]
rs2707472	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707473	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707474	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707475	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707476	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707482	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707492	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707503	0.90[ASN][1000 genomes]
rs2707504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707516	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908006	0.94[ASN][1000 genomes]
rs2908010	0.94[ASN][1000 genomes]
rs2952564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727922	0.84[EUR][1000 genomes]
rs56293108	0.97[ASN][1000 genomes]
rs57275855	0.94[ASN][1000 genomes]
rs60736586	0.97[ASN][1000 genomes]
rs62476334	0.83[ASN][1000 genomes]
rs6943521	0.85[ASN][1000 genomes]
rs6954568	0.88[ASN][1000 genomes]
rs6956903	0.93[ASN][1000 genomes]
rs6972181	0.94[ASN][1000 genomes]
rs6972247	0.88[ASN][1000 genomes]
rs71571022	0.85[EUR][1000 genomes]
rs73440208	0.94[ASN][1000 genomes]
rs73440215	0.94[ASN][1000 genomes]
rs73440221	0.97[ASN][1000 genomes]
rs73720406	0.97[ASN][1000 genomes]
rs7780789	0.94[ASN][1000 genomes]
rs7782648	0.94[ASN][1000 genomes]
rs7785478	1.00[ASN][1000 genomes]
rs7792993	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10250907	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120970800-121000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:120978600-120994600	Weak transcription	Fetal Thymus	thymus
7	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:120979400-120995400	Weak transcription	Fetal Heart	heart
9	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
10	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:120981000-121015200	Weak transcription	Pancreas	Pancrea
13	chr7:120983000-120996600	Weak transcription	Fetal Lung	lung
14	chr7:120983000-121009600	Weak transcription	Hela-S3	cervix
15	chr7:120983800-120994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:120983800-121000200	Weak transcription	Fetal Kidney	kidney
17	chr7:120984000-120993200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:120984000-121017600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:120984200-121001200	Weak transcription	NHLF	lung
20	chr7:120984200-121009800	Weak transcription	Fetal Brain Male	brain
21	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:120984800-120994600	Weak transcription	Brain Angular Gyrus	brain
23	chr7:120984800-121009600	Weak transcription	A549	lung
24	chr7:120985000-120995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:120985000-120995800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:120985000-121001200	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:120985000-121009600	Weak transcription	Small Intestine	intestine
28	chr7:120985200-121000000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:120985200-121013000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:120985400-120995800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:120986200-121029600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:120986400-120996200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:120986400-121026000	Weak transcription	Colonic Mucosa	Colon
34	chr7:120986400-121026000	Weak transcription	Psoas Muscle	Psoas
35	chr7:120987000-120993600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr7:120987400-120993400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:120987600-120992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:120987600-120992800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:120987600-120993200	Weak transcription	GM12878-XiMat	blood
40	chr7:120987600-120995000	Weak transcription	Adipose Nuclei	Adipose
41	chr7:120987600-120995400	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:120987600-120995400	Weak transcription	NHEK	skin
43	chr7:120987600-120996600	Weak transcription	K562	blood
44	chr7:120987600-121003800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:120989200-120999000	Weak transcription	HepG2	liver
46	chr7:120989200-121015400	Weak transcription	Brain Anterior Caudate	brain
47	chr7:120989600-121016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr7:120989800-120996400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:120990400-120993400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:120990400-120994800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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