Variant report

Variant	rs7662650
Chromosome Location	chr4:119705915-119705916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119704843..119706853-chr4:119753213..119755649,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11724866	0.84[EUR][1000 genomes]
rs11730728	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11735989	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11945703	0.84[EUR][1000 genomes]
rs12640223	0.84[EUR][1000 genomes]
rs12646268	0.82[EUR][1000 genomes]
rs12646298	0.83[EUR][1000 genomes]
rs12648682	0.84[EUR][1000 genomes]
rs12648778	0.84[EUR][1000 genomes]
rs13105145	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13105732	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13111664	0.84[EUR][1000 genomes]
rs13115157	0.84[EUR][1000 genomes]
rs13124091	0.84[EUR][1000 genomes]
rs13146440	0.88[EUR][1000 genomes]
rs13146816	0.87[EUR][1000 genomes]
rs13150663	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029399	0.81[EUR][1000 genomes]
rs2046779	0.86[EUR][1000 genomes]
rs2288307	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087958	0.84[EUR][1000 genomes]
rs34091082	0.86[EUR][1000 genomes]
rs34270389	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34508500	0.86[EUR][1000 genomes]
rs34628947	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35023705	0.84[EUR][1000 genomes]
rs35071348	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35392662	0.87[EUR][1000 genomes]
rs35404779	0.87[EUR][1000 genomes]
rs35522890	0.84[EUR][1000 genomes]
rs35613641	0.84[EUR][1000 genomes]
rs35952841	0.84[EUR][1000 genomes]
rs36023173	0.84[EUR][1000 genomes]
rs3733517	0.84[EUR][1000 genomes]
rs66500248	0.84[EUR][1000 genomes]
rs66942289	0.84[EUR][1000 genomes]
rs67151421	0.85[EUR][1000 genomes]
rs67989872	0.86[EUR][1000 genomes]
rs6813357	0.84[EUR][1000 genomes]
rs6814447	0.84[EUR][1000 genomes]
rs6817790	0.84[EUR][1000 genomes]
rs6818241	0.84[EUR][1000 genomes]
rs6821350	0.84[EUR][1000 genomes]
rs6827740	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829010	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831197	0.84[EUR][1000 genomes]
rs6836005	0.84[EUR][1000 genomes]
rs6837652	0.84[EUR][1000 genomes]
rs6847706	0.87[EUR][1000 genomes]
rs6849714	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6852706	0.83[EUR][1000 genomes]
rs6853722	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855919	0.84[EUR][1000 genomes]
rs6857285	0.87[EUR][1000 genomes]
rs71610228	0.84[EUR][1000 genomes]
rs72679023	0.87[EUR][1000 genomes]
rs7653962	0.88[EUR][1000 genomes]
rs7670182	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681835	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7692721	0.84[EUR][1000 genomes]
rs7695602	0.87[EUR][1000 genomes]
rs7696543	0.87[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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7662650	RP11-384K6.6	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
2	chr4:119678600-119717400	Weak transcription	Esophagus	oesophagus
3	chr4:119679000-119717600	Weak transcription	Colonic Mucosa	Colon
4	chr4:119687600-119711800	Weak transcription	Stomach Mucosa	stomach
5	chr4:119688600-119710000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:119688600-119712800	Weak transcription	Gastric	stomach
7	chr4:119688600-119715800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:119688600-119717400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:119688600-119717400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:119688600-119732600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:119688800-119716800	Weak transcription	Fetal Kidney	kidney
12	chr4:119689400-119709000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:119689400-119716200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:119689400-119716600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:119689400-119716800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:119689600-119709400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:119689600-119717600	Weak transcription	K562	blood
18	chr4:119689800-119708800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:119690000-119717600	Weak transcription	Primary T cells from cord blood	blood
20	chr4:119694000-119715000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:119694000-119717400	Weak transcription	Ovary	ovary
22	chr4:119694400-119716600	Weak transcription	Aorta	Aorta
23	chr4:119695000-119710000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:119695000-119717600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:119696400-119715600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:119696800-119717400	Weak transcription	Spleen	Spleen
27	chr4:119698000-119706800	Weak transcription	HUVEC	blood vessel
28	chr4:119698000-119709400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:119698200-119712200	Weak transcription	Adipose Nuclei	Adipose
30	chr4:119702400-119706000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:119702600-119717600	Weak transcription	Fetal Brain Male	brain
32	chr4:119703000-119711000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:119703400-119706000	Strong transcription	Fetal Stomach	stomach
34	chr4:119703400-119706400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:119703400-119732200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:119703600-119706400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:119703600-119706600	Strong transcription	Liver	Liver
38	chr4:119703800-119738200	Strong transcription	Placenta	Placenta
39	chr4:119704000-119706800	Strong transcription	Dnd41	blood
40	chr4:119704000-119710000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:119704200-119712600	Strong transcription	NH-A	brain
42	chr4:119704200-119713000	Weak transcription	Lung	lung
43	chr4:119704200-119740000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:119704400-119706400	Strong transcription	HSMM	muscle
45	chr4:119704400-119708200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:119704400-119714000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:119704400-119717600	Weak transcription	Pancreas	Pancrea
48	chr4:119704600-119706600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:119704600-119706800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:119704600-119708400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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