Variant report

Variant	rs913861
Chromosome Location	chr1:153622220-153622221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153505419..153507126-chr1:153619348..153622269,2	K562	blood:
2	chr1:153542770..153546215-chr1:153620036..153623245,5	MCF-7	breast:
3	chr1:153622142..153624263-chr1:153962051..153964552,2	MCF-7	breast:
4	chr1:153490604..153493387-chr1:153620859..153622534,2	MCF-7	breast:
5	chr1:153621962..153623668-chr6:15660534..15662735,2	MCF-7	breast:
6	chr1:153621742..153623509-chr1:153747385..153749734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046381	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10797056	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797090	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10797096	0.88[JPT][hapmap]
rs10908746	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908848	0.88[JPT][hapmap]
rs11265625	0.88[JPT][hapmap]
rs11265633	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1128894	0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11497739	0.82[TSI][hapmap]
rs11548103	0.83[EUR][1000 genomes]
rs11548104	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs11580122	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12139953	0.88[ASN][1000 genomes]
rs12564925	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12730186	0.91[ASN][1000 genomes]
rs1411273	0.81[EUR][1000 genomes]
rs1810836	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1888115	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274739	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274740	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28379831	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28380060	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28416529	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28510471	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28518786	0.89[ASN][1000 genomes]
rs28580554	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28613361	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28700217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28754733	0.80[CHD][hapmap]
rs3790411	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790412	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795396	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806233	0.83[CHD][hapmap]
rs3806234	0.80[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3818632	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828031	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862047	0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4351684	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4515830	0.89[JPT][hapmap]
rs4845557	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845558	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845560	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6427640	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66721814	0.88[ASN][1000 genomes]
rs6674929	0.88[JPT][hapmap]
rs6694006	0.82[AMR][1000 genomes]
rs7345	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541193	0.80[MEX][hapmap]
rs7934	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs913860	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9330298	0.84[CHB][hapmap]
rs9330299	0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs9661993	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9662664	0.88[JPT][hapmap]
rs9729773	0.83[EUR][1000 genomes]
rs985242	0.81[EUR][1000 genomes]
rs999418	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription 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	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs913861	S100A13	cis	parietal	SCAN
rs913861	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs913861	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs913861	S100A13	cis	multi-tissue	Pritchard
rs913861	CHTOP	cis	Muscle Skeletal	GTEx
rs913861	SLC27A3	cis	cerebellum	SCAN
rs913861	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs913861	RP1-178F15.4	cis	lung	GTEx
rs913861	S100A2	cis	cerebellum	SCAN
rs913861	S100A10	cis	cerebellum	SCAN
rs913861	RP1-178F15.4	cis	Artery Aorta	GTEx
rs913861	C1orf77	cis	multi-tissue	Pritchard
rs913861	S100A13	cis	Adipose Subcutaneous	GTEx
rs913861	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs913861	S100A16	cis	parietal	SCAN
rs913861	S100A16	cis	cerebellum	SCAN
rs913861	S100A13	cis	lymphoblastoid	seeQTL
rs913861	S100A13	cis	Lymphoblastoid	GTEx
rs913861	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153611000-153622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153618400-153625400	Weak transcription	Small Intestine	intestine
3	chr1:153618400-153630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:153618400-153631200	Weak transcription	Aorta	Aorta
5	chr1:153618600-153622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153618600-153631000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:153618600-153631000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:153618800-153622400	Weak transcription	Fetal Lung	lung
9	chr1:153618800-153625000	Weak transcription	Hela-S3	cervix
10	chr1:153618800-153625000	Weak transcription	HUVEC	blood vessel
11	chr1:153618800-153625200	Weak transcription	NHDF-Ad	bronchial
12	chr1:153618800-153625400	Weak transcription	NH-A	brain
13	chr1:153618800-153626400	Weak transcription	HepG2	liver
14	chr1:153618800-153630800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:153619000-153625000	Weak transcription	Colonic Mucosa	Colon
16	chr1:153619200-153623400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:153619200-153630800	Weak transcription	Fetal Kidney	kidney
18	chr1:153619400-153625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:153619400-153625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:153619600-153622600	Enhancers	K562	blood
21	chr1:153619600-153624400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:153619600-153625000	Weak transcription	HMEC	breast
23	chr1:153619600-153625000	Weak transcription	Osteobl	bone
24	chr1:153619600-153625400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:153619600-153630800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:153619800-153623000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:153619800-153625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:153619800-153625200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:153619800-153625200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:153620000-153625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:153620000-153625000	Weak transcription	NHEK	skin
32	chr1:153620000-153625200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:153620000-153625200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:153620000-153630400	Weak transcription	Dnd41	blood
35	chr1:153620000-153630400	Weak transcription	GM12878-XiMat	blood
36	chr1:153620200-153622600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:153620200-153623600	Enhancers	Pancreas	Pancrea
38	chr1:153620200-153624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:153620200-153625000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:153620200-153625000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:153620200-153625000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:153620200-153625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:153620200-153625200	Weak transcription	A549	lung
44	chr1:153620200-153625200	Weak transcription	NHLF	lung
45	chr1:153620200-153630400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:153620200-153630400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:153620200-153630600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:153620200-153630600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:153620200-153630600	Weak transcription	Primary B cells from cord blood	blood
50	chr1:153620200-153631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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