Variant report

Variant	rs11111817
Chromosome Location	chr12:104254932-104254933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104252726..104255857-chr12:104256920..104259686,3	MCF-7	breast:
2	chr12:104252720..104255183-chr12:104502836..104504925,2	K562	blood:
3	chr12:104234105..104239098-chr12:104250004..104255076,13	MCF-7	breast:
4	chr12:104164135..104167659-chr12:104253252..104255970,3	MCF-7	breast:
5	chr12:104176628..104179392-chr12:104253819..104256321,2	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10745982	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10745983	0.83[EUR][1000 genomes]
rs10778291	0.84[EUR][1000 genomes]
rs10778293	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs10778294	0.85[EUR][1000 genomes]
rs10778295	0.83[EUR][1000 genomes]
rs10861124	0.87[JPT][hapmap]
rs10861128	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10861129	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11111816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111858	0.87[JPT][hapmap]
rs1165596	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1165597	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1165598	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs1165666	0.88[JPT][hapmap]
rs1165677	0.88[JPT][hapmap]
rs1165678	0.88[JPT][hapmap]
rs1165682	0.88[JPT][hapmap]
rs1183212	0.88[JPT][hapmap]
rs1185985	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12312978	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs12368121	0.82[JPT][hapmap]
rs12368164	0.81[JPT][hapmap]
rs1583599	0.85[EUR][1000 genomes]
rs1595338	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1595339	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1866070	0.87[JPT][hapmap]
rs2196614	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2248382	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2251979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252000	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374353	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2438116	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439622	0.84[EUR][1000 genomes]
rs2576950	0.84[EUR][1000 genomes]
rs2576957	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2576958	0.84[EUR][1000 genomes]
rs2576960	0.84[EUR][1000 genomes]
rs2576961	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2576962	0.84[EUR][1000 genomes]
rs2576963	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2576964	0.84[EUR][1000 genomes]
rs2576965	0.83[EUR][1000 genomes]
rs2576967	0.83[EUR][1000 genomes]
rs2576970	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs2583240	0.84[EUR][1000 genomes]
rs2583241	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2583242	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2583243	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2583245	0.84[CEU][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2583246	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2583247	0.84[EUR][1000 genomes]
rs2583248	0.84[EUR][1000 genomes]
rs2583250	0.81[EUR][1000 genomes]
rs4316574	0.84[EUR][1000 genomes]
rs4488278	0.84[EUR][1000 genomes]
rs4556622	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs6539104	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs728165	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7301119	0.94[ASN][1000 genomes]
rs7302074	0.88[JPT][hapmap]
rs7957036	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs7967501	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111817	SLC5A8	cis	parietal	SCAN
rs11111817	GNN	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104250000-104257000	Weak transcription	Pancreas	Pancrea
2	chr12:104250000-104263800	Weak transcription	Liver	Liver
3	chr12:104252200-104255000	Enhancers	HMEC	breast
4	chr12:104252200-104255800	Enhancers	Placenta	Placenta
5	chr12:104252400-104255000	Enhancers	Colon Smooth Muscle	Colon
6	chr12:104252600-104255000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:104253600-104261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:104254000-104258600	Weak transcription	HSMMtube	muscle
9	chr12:104254400-104255400	Weak transcription	Fetal Stomach	stomach
10	chr12:104254400-104255600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:104254400-104256800	Weak transcription	Ovary	ovary
12	chr12:104254400-104256800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:104254400-104257600	Weak transcription	Esophagus	oesophagus
14	chr12:104254400-104257800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:104254400-104258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:104254400-104258000	Weak transcription	NHEK	skin
17	chr12:104254400-104258600	Weak transcription	HSMM	muscle
18	chr12:104254400-104258800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:104254600-104255000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:104254600-104256200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:104254800-104255000	Enhancers	Osteobl	bone
22	chr12:104254800-104255200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:104254800-104255200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:104254800-104255600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:104254800-104256200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:104254800-104278200	Weak transcription	Aorta	Aorta

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