Variant report

Variant	rs7934
Chromosome Location	chr1:153618766-153618767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153617772..153619416-chr1:153733072..153735743,2	K562	blood:
2	chr1:153616663..153619179-chr1:153636711..153638516,2	MCF-7	breast:
3	chr1:153616510..153622201-chr1:153629664..153635649,10	MCF-7	breast:
4	chr1:153617865..153619831-chr1:153713575..153715568,2	K562	blood:
5	chr1:153507610..153510354-chr1:153617005..153619352,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197956	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143621	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1046381	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10797056	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797090	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10797096	0.88[JPT][hapmap]
rs10908746	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908848	0.88[JPT][hapmap]
rs11265625	0.88[JPT][hapmap]
rs11265633	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1128894	0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11497739	0.82[TSI][hapmap]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11580122	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139953	0.88[ASN][1000 genomes]
rs12564925	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12730186	0.91[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes]
rs1810836	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1888115	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274739	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274740	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28379831	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28380060	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28416529	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28510471	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28518786	0.90[ASN][1000 genomes]
rs28580554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28613361	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28700217	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28754733	0.83[CHD][hapmap]
rs3790411	0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3790412	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795396	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806233	0.93[CHD][hapmap]
rs3806234	0.90[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3818632	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828031	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862047	0.86[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4351684	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4515830	0.89[JPT][hapmap]
rs4845557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845558	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.80[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6427640	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66721814	0.88[ASN][1000 genomes]
rs6674929	0.88[JPT][hapmap]
rs6694006	0.85[AMR][1000 genomes]
rs7345	0.92[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541193	0.80[MEX][hapmap]
rs913860	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs913861	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]
rs9330299	0.80[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9661993	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9662664	0.88[JPT][hapmap]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes]
rs999418	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7934	CHTOP	cis	Muscle Skeletal	GTEx
rs7934	S100A10	cis	cerebellum	SCAN
rs7934	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs7934	S100A2	cis	cerebellum	SCAN
rs7934	RP1-178F15.4	cis	Artery Aorta	GTEx
rs7934	S100A16	cis	parietal	SCAN
rs7934	S100A13	cis	parietal	SCAN
rs7934	FLG	cis	cerebellum	SCAN
rs7934	RP1-178F15.4	cis	lung	GTEx
rs7934	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs7934	S100A16	cis	cerebellum	SCAN
rs7934	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs7934	S100A13	cis	Adipose Subcutaneous	GTEx
rs7934	SLC27A3	cis	cerebellum	SCAN
rs7934	S100A4	cis	lymphoblastoid	seeQTL
rs7934	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs7934	S100A13	cis	lymphoblastoid	seeQTL
rs7934	S100A13	cis	multi-tissue	Pritchard
rs7934	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs7934	S100A13	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153608200-153618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:153608200-153619600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:153608400-153618800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr1:153608400-153618800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:153608400-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:153608400-153619200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:153608400-153619800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:153608600-153618800	Strong transcription	HUVEC	blood vessel
9	chr1:153608600-153619400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:153608600-153619400	Strong transcription	Osteobl	bone
11	chr1:153608600-153619600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr1:153608600-153619600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:153608600-153619600	Strong transcription	HMEC	breast
14	chr1:153608600-153620200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:153608600-153620200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:153608800-153618800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:153608800-153619400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:153608800-153619800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:153608800-153620200	Strong transcription	Fetal Thymus	thymus
20	chr1:153609200-153618800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:153609200-153619400	Strong transcription	Spleen	Spleen
22	chr1:153609200-153620000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:153609200-153620000	Strong transcription	Fetal Brain Female	brain
24	chr1:153609200-153620200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:153609400-153618800	Strong transcription	Fetal Lung	lung
26	chr1:153609400-153618800	Strong transcription	NH-A	brain
27	chr1:153609400-153619000	Strong transcription	Thymus	Thymus
28	chr1:153609600-153618800	Strong transcription	Placenta	Placenta
29	chr1:153609600-153618800	Strong transcription	K562	blood
30	chr1:153609600-153618800	Strong transcription	NHDF-Ad	bronchial
31	chr1:153609600-153619000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:153609600-153619200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:153609600-153619200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:153609600-153619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:153609600-153619400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr1:153609600-153619400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:153609600-153619800	Weak transcription	Right Atrium	heart
38	chr1:153609600-153620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:153609600-153620000	Strong transcription	Brain Germinal Matrix	brain
40	chr1:153609600-153620000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:153609600-153620200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:153609600-153620200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:153609600-153620200	Strong transcription	HSMM	muscle
44	chr1:153609600-153620200	Strong transcription	NHLF	lung
45	chr1:153609600-153620800	Strong transcription	Fetal Stomach	stomach
46	chr1:153609800-153620000	Strong transcription	NHEK	skin
47	chr1:153609800-153620200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr1:153610000-153619600	Strong transcription	Lung	lung
49	chr1:153610200-153619400	Strong transcription	Gastric	stomach
50	chr1:153610200-153619600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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