Variant report

Variant	rs7938498
Chromosome Location	chr11:63729790-63729791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62607799..62609460-chr11:63729249..63731107,2	MCF-7	breast:
2	chr11:63727902..63730115-chr11:63749868..63752582,2	MCF-7	breast:
3	chr11:63727931..63732327-chr11:63736906..63740363,4	K562	blood:
4	chr11:63724309..63727008-chr11:63727662..63729826,2	MCF-7	breast:
5	chr11:63727872..63730368-chr11:63752285..63755154,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000167770	Chromatin interaction
ENSG00000207200	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10751004	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10792424	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10897459	0.81[TSI][hapmap]
rs10897464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10897466	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs10897467	0.83[EUR][1000 genomes]
rs10897468	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897470	0.81[EUR][1000 genomes]
rs11231646	0.87[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231653	0.94[EUR][1000 genomes]
rs11231662	0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11231663	0.82[EUR][1000 genomes]
rs11231664	0.81[EUR][1000 genomes]
rs11231670	0.81[EUR][1000 genomes]
rs11231671	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11600062	0.81[EUR][1000 genomes]
rs11601228	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11605797	0.83[TSI][hapmap]
rs11607028	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12417157	0.82[EUR][1000 genomes]
rs12790749	0.96[EUR][1000 genomes]
rs12798491	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs12800703	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12808604	0.97[EUR][1000 genomes]
rs1386346	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1684950	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1783964	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129467	0.81[EUR][1000 genomes]
rs2318110	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508584	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3019782	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs320121	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs320156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34134698	0.80[EUR][1000 genomes]
rs35492216	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740636	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3740637	0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4426138	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs479975	0.80[EUR][1000 genomes]
rs480211	0.83[CHB][hapmap]
rs481835	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs483340	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs487540	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs488082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs492357	0.81[EUR][1000 genomes]
rs4980499	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4980500	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4980509	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4980512	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4980516	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4980517	0.80[EUR][1000 genomes]
rs4980530	0.81[TSI][hapmap]
rs499118	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs500493	0.93[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs502858	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504060	0.80[EUR][1000 genomes]
rs504314	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs509701	0.81[MEX][hapmap];0.80[TSI][hapmap]
rs528927	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs529915	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539432	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs540389	0.83[CHB][hapmap]
rs553724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs567386	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs578295	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591830	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709594	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7111130	0.82[EUR][1000 genomes]
rs728919	0.93[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];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7926608	0.83[EUR][1000 genomes]
rs7928990	0.95[EUR][1000 genomes]
rs7936614	0.82[EUR][1000 genomes]
rs7942318	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7951529	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9943682	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
7	nsv897639	chr11:63691049-63844683	Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7938498	FTH1	cis	parietal	SCAN
rs7938498	HNRNPUL2	cis	parietal	SCAN
rs7938498	PLCB3	cis	cerebellum	SCAN
rs7938498	RBM4B	cis	cerebellum	SCAN
rs7938498	SLC22A24	cis	parietal	SCAN
rs7938498	GPR137	cis	parietal	SCAN
rs7938498	EHD1	cis	parietal	SCAN
rs7938498	SLC15A3	cis	parietal	SCAN
rs7938498	SLC22A12	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63713400-63733800	Weak transcription	Right Atrium	heart
2	chr11:63723800-63730000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:63724200-63732600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:63724200-63733200	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:63724200-63734800	Weak transcription	Ovary	ovary
6	chr11:63725200-63730000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:63725400-63732600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:63726400-63730000	Weak transcription	Fetal Brain Female	brain
9	chr11:63727200-63729800	Enhancers	HepG2	liver
10	chr11:63727200-63730000	Enhancers	Fetal Intestine Small	intestine
11	chr11:63727200-63730400	Enhancers	Fetal Thymus	thymus
12	chr11:63727200-63730600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:63727400-63730400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:63727400-63730600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:63727600-63730600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr11:63727600-63730600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:63728200-63729800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr11:63728200-63730000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:63728200-63730000	Enhancers	Dnd41	blood
20	chr11:63728200-63730400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:63728200-63730600	Enhancers	Fetal Muscle Leg	muscle
22	chr11:63728200-63731400	Enhancers	GM12878-XiMat	blood
23	chr11:63728400-63729800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:63728400-63730000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:63728400-63730200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:63728400-63730200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:63728400-63730200	Enhancers	Placenta	Placenta
28	chr11:63728400-63730200	Enhancers	NHEK	skin
29	chr11:63728400-63730400	Enhancers	Fetal Stomach	stomach
30	chr11:63728400-63730400	Enhancers	HSMM	muscle
31	chr11:63728400-63730800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:63728600-63729800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:63728600-63729800	Enhancers	Esophagus	oesophagus
34	chr11:63728600-63730000	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:63728600-63730200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:63728600-63730200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:63728600-63730200	Enhancers	HMEC	breast
38	chr11:63728800-63729800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:63728800-63730000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:63728800-63730000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:63728800-63730000	Enhancers	Stomach Smooth Muscle	stomach
42	chr11:63728800-63730000	Enhancers	HSMMtube	muscle
43	chr11:63728800-63730000	Enhancers	NHLF	lung
44	chr11:63729000-63729800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:63729000-63729800	Enhancers	Fetal Lung	lung
46	chr11:63729000-63729800	Enhancers	Gastric	stomach
47	chr11:63729000-63729800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr11:63729000-63729800	Enhancers	Thymus	Thymus
49	chr11:63729000-63729800	Enhancers	NHDF-Ad	bronchial
50	chr11:63729000-63730000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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