Variant report

Variant	rs2707460
Chromosome Location	chr7:120986360-120986361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120986190..120988228-chr7:120994808..120997127,2	K562	blood:
2	chr7:120985694..120988582-chr7:121034968..121037690,2	K562	blood:
3	chr7:120984176..120986592-chr7:121005474..121007076,2	MCF-7	breast:
4	chr7:120969341..120972493-chr7:120983934..120987124,3	K562	blood:
5	chr7:120983315..120988204-chr7:120988665..120992990,4	K562	blood:
6	chr7:120983770..120986727-chr7:120991532..120993657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10250624	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10250907	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11762263	0.98[EUR][1000 genomes]
rs11762452	0.94[EUR][1000 genomes]
rs11768996	0.93[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs11770098	0.91[EUR][1000 genomes]
rs11771477	0.91[EUR][1000 genomes]
rs12706336	0.91[EUR][1000 genomes]
rs12706337	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs12706338	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12706339	0.93[EUR][1000 genomes]
rs12706340	0.90[EUR][1000 genomes]
rs12706341	0.93[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs12706342	0.90[EUR][1000 genomes]
rs12706343	0.80[EUR][1000 genomes]
rs12706346	1.00[CHD][hapmap]
rs13238085	0.93[EUR][1000 genomes]
rs17143305	0.93[EUR][1000 genomes]
rs1803389	0.98[EUR][1000 genomes]
rs1990446	0.88[ASW][hapmap];0.93[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1990447	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2041490	0.85[CEU][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs2254591	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536153	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2536155	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536156	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536157	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2536158	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536159	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536160	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536163	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536164	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536165	0.93[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536166	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536167	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536168	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536170	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536173	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536174	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536175	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536176	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536178	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536179	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536184	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536188	0.85[EUR][1000 genomes]
rs2536190	0.85[EUR][1000 genomes]
rs2536192	0.86[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2707461	0.88[ASW][hapmap];0.93[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707462	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707463	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707465	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2707467	0.85[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2707468	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707469	0.86[TSI][hapmap]
rs2707470	0.84[EUR][1000 genomes]
rs2707471	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707472	0.86[EUR][1000 genomes]
rs2707473	0.84[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2707474	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2707475	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707476	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707477	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707478	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707479	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707480	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707481	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2707482	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707491	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707492	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707496	0.88[ASW][hapmap];0.93[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707504	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707505	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707507	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707516	0.85[EUR][1000 genomes]
rs2952564	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4727922	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs4727925	0.80[EUR][1000 genomes]
rs4731011	0.80[EUR][1000 genomes]
rs71571022	0.94[EUR][1000 genomes]
rs7792993	0.93[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs997782	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2707460	FAM3C	cis	lymphoblastoid	seeQTL
rs2707460	FAM3C	Cis_1M	lymphoblastoid	RTeQTL
rs2707460	HYAL4	cis	cerebellum	SCAN

Chromatin state (count:108 , 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	chr7:120971000-120986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:120972000-120986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:120972000-120992400	Weak transcription	Esophagus	oesophagus
7	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:120974800-120986400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:120975600-120992400	Weak transcription	HSMMtube	muscle
10	chr7:120976400-120986800	Weak transcription	Fetal Brain Female	brain
11	chr7:120977400-120987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:120977600-120992400	Weak transcription	Fetal Intestine Small	intestine
13	chr7:120977800-120986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:120978000-120986400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:120978600-120986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:120978600-120990600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:120978600-120994600	Weak transcription	Fetal Thymus	thymus
19	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:120979400-120986600	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:120979400-120990400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:120979400-120992400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:120979400-120992400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:120979400-120992400	Weak transcription	Lung	lung
25	chr7:120979400-120995400	Weak transcription	Fetal Heart	heart
26	chr7:120979600-120986800	Weak transcription	K562	blood
27	chr7:120979600-120992400	Weak transcription	Aorta	Aorta
28	chr7:120979800-120986600	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:120979800-120986600	Weak transcription	HMEC	breast
30	chr7:120979800-120986800	Weak transcription	Right Ventricle	heart
31	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
32	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:120980000-120992000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:120980200-120986800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:120980200-120986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:120980400-120987200	Weak transcription	GM12878-XiMat	blood
37	chr7:120980400-120992400	Weak transcription	Fetal Stomach	stomach
38	chr7:120980400-120992600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:120980600-120986800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:120980600-120990600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr7:120980800-120986400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:120981000-120986400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:120981000-120992400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:120981000-121015200	Weak transcription	Pancreas	Pancrea
46	chr7:120981200-120990800	Weak transcription	Placenta	Placenta
47	chr7:120982000-120986600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:120982000-120987800	Strong transcription	Primary B cells from cord blood	blood
49	chr7:120983000-120986600	Weak transcription	HSMM	muscle
50	chr7:120983000-120986800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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