Variant report

Variant	rs3767964
Chromosome Location	chr1:93815490-93815491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:93815369-93815522	GM12878	blood:	n/a	n/a
2	EP300	chr1:93815322-93815627	GM12878	blood:	n/a	n/a
3	USF2	chr1:93815458-93815632	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93809993..93812925-chr1:93814019..93816976,3	MCF-7	breast:
2	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
3	chr1:93813688..93816187-chr1:93818806..93820791,2	MCF-7	breast:
4	chr1:93810887..93813199-chr1:93813270..93816072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	TF binding region
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1000607	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060622	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10782955	0.80[EUR][1000 genomes]
rs10782957	0.85[ASN][1000 genomes]
rs10782959	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs10874764	0.80[EUR][1000 genomes]
rs10874772	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874773	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874777	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874778	0.82[ASN][1000 genomes]
rs1088318	0.82[ASN][1000 genomes]
rs11164876	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs11164879	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs11164881	0.80[EUR][1000 genomes]
rs11164902	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164904	0.85[ASN][1000 genomes]
rs11164908	0.87[CHB][hapmap]
rs11164916	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11164938	0.90[JPT][hapmap]
rs11576494	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030549	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs12030843	0.87[CHB][hapmap]
rs12033147	0.85[CHB][hapmap]
rs12044557	0.86[CHB][hapmap]
rs12044883	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118230	0.80[EUR][1000 genomes]
rs12118262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs12124011	0.80[EUR][1000 genomes]
rs12124771	0.87[ASN][1000 genomes]
rs12133576	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133907	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12135266	0.90[JPT][hapmap]
rs12138486	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12139633	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12406245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12563120	0.86[CHB][hapmap]
rs12742850	0.90[JPT][hapmap]
rs12752223	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335679	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs1426318	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535699	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1535701	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559828	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1593512	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1812668	0.90[JPT][hapmap]
rs2031225	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2031226	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114273	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255722	0.82[CHB][hapmap]
rs2296558	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2391254	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391256	0.82[ASN][1000 genomes]
rs2391271	0.84[JPT][hapmap]
rs2484486	0.81[CHB][hapmap]
rs2765545	0.91[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs2783489	0.95[CHB][hapmap]
rs2783490	0.82[CHB][hapmap]
rs2783495	0.82[CHB][hapmap]
rs2783499	0.86[CHB][hapmap]
rs2783500	0.86[CHB][hapmap]
rs2783501	0.87[CHB][hapmap]
rs35628716	0.81[ASN][1000 genomes]
rs35915989	0.80[ASN][1000 genomes]
rs3754186	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3767962	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767967	0.90[JPT][hapmap]
rs3904666	0.82[CHB][hapmap]
rs4000699	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4484937	0.86[CHB][hapmap]
rs4847235	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs4847240	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847245	0.90[JPT][hapmap]
rs4847406	0.85[ASN][1000 genomes]
rs4847408	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847410	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847412	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847419	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847420	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847428	0.90[JPT][hapmap]
rs531358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs531514	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs535760	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs547866	0.82[ASN][1000 genomes]
rs555161	0.82[EUR][1000 genomes]
rs569414	0.91[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59417472	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602204	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs612037	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs622608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs627779	0.80[EUR][1000 genomes]
rs637646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6541349	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6541401	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541404	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6658257	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680022	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6680107	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682670	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs6694508	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6703310	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs682514	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs687394	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs693737	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs698927	0.81[ASN][1000 genomes]
rs7417952	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7418101	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7512911	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7513705	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs7517363	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7524964	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7525248	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526112	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7535628	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs7537403	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539307	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs7540025	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541304	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541687	0.80[EUR][1000 genomes]
rs7547244	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551485	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs771458	0.81[ASN][1000 genomes]
rs771462	0.81[ASN][1000 genomes]
rs771481	0.91[CHB][hapmap]
rs797661	0.83[EUR][1000 genomes]
rs797666	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797668	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs797671	0.83[EUR][1000 genomes]
rs797672	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797680	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs797681	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs810027	0.82[CHB][hapmap]
rs942196	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9432453	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432459	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432465	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432681	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3767964	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs3767964	RP4-717I23.3	cis	Whole Blood	GTEx
rs3767964	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs3767964	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs3767964	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs3767964	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs3767964	DR1	cis	multi-tissue	Pritchard
rs3767964	RP4-717I23.3	cis	lung	GTEx
rs3767964	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs3767964	DR1	cis	Adipose Subcutaneous	GTEx
rs3767964	RP4-717I23.3	cis	Thyroid	GTEx
rs3767964	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs3767964	RP4-717I23.3	cis	Artery Tibial	GTEx
rs3767964	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93809800-93817200	Active TSS	GM12878-XiMat	blood
2	chr1:93810200-93815600	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:93810400-93815600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:93810400-93815600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:93810400-93815600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:93810400-93816200	Active TSS	HSMMtube	muscle
7	chr1:93810600-93815600	Active TSS	Fetal Muscle Leg	muscle
8	chr1:93810600-93815600	Active TSS	Fetal Thymus	thymus
9	chr1:93810600-93815600	Active TSS	Right Atrium	heart
10	chr1:93810600-93815800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:93810600-93815800	Active TSS	Thymus	Thymus
12	chr1:93810800-93815600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:93810800-93815800	Active TSS	HMEC	breast
14	chr1:93811600-93816600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:93812000-93815600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:93812000-93816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:93812200-93815600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:93812600-93817200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:93812800-93815600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:93812800-93815800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:93812800-93815800	Weak transcription	Small Intestine	intestine
22	chr1:93812800-93823800	Weak transcription	Spleen	Spleen
23	chr1:93812800-93831000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:93812800-93832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:93813000-93817000	Weak transcription	Esophagus	oesophagus
26	chr1:93813000-93817000	Weak transcription	Lung	lung
27	chr1:93813000-93817000	Weak transcription	Pancreas	Pancrea
28	chr1:93813000-93823800	Weak transcription	Gastric	stomach
29	chr1:93813400-93815600	Flanking Active TSS	Liver	Liver
30	chr1:93813400-93816600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr1:93813400-93817000	Weak transcription	Left Ventricle	heart
32	chr1:93813400-93817000	Weak transcription	Ovary	ovary
33	chr1:93813400-93820200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:93813600-93815800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:93813800-93816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:93814000-93815600	Flanking Active TSS	HUVEC	blood vessel
39	chr1:93814200-93815600	Active TSS	Brain Anterior Caudate	brain
40	chr1:93814200-93816600	Enhancers	Brain Cingulate Gyrus	brain
41	chr1:93814200-93816800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr1:93814200-93816800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:93814200-93817000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:93814200-93819200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:93814200-93823600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:93814200-93823800	Weak transcription	Right Ventricle	heart
47	chr1:93814400-93815600	Active TSS	Brain Hippocampus Middle	brain
48	chr1:93814400-93816000	Enhancers	Fetal Heart	heart
49	chr1:93814400-93816800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:93814400-93817000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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