Variant report

Variant	rs6465890
Chromosome Location	chr7:102717712-102717713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102714716..102718005-chr7:102734624..102737524,3	MCF-7	breast:
2	chr7:102715242..102717974-chr7:105515259..105517980,2	MCF-7	breast:
3	chr7:102715629..102718160-chr7:102729461..102731149,2	K562	blood:
4	chr7:102714987..102719162-chr7:102758108..102764327,6	K562	blood:
5	chr7:102713351..102719247-chr7:102725221..102729310,7	MCF-7	breast:
6	chr20:53057077..53059223-chr7:102716078..102718486,2	MCF-7	breast:
7	chr7:102714071..102718258-chr7:102757961..102760938,3	K562	blood:

Variant related genes	Relation type
ENSG00000146776	Chromatin interaction
ENSG00000161048	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000233025	Chromatin interaction
ENSG00000128536	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10268849	1.00[MEX][hapmap]
rs10278727	1.00[MEX][hapmap]
rs10808121	1.00[MEX][hapmap]
rs10808122	0.90[AFR][1000 genomes]
rs10808123	0.91[AFR][1000 genomes]
rs10808125	0.85[YRI][hapmap]
rs10953378	0.85[AFR][1000 genomes]
rs11532769	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs11543780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11560367	0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap]
rs11560368	0.83[CHB][hapmap]
rs11560369	1.00[CEU][hapmap]
rs11981558	0.91[AFR][1000 genomes]
rs12673840	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs13225565	0.91[YRI][hapmap]
rs13242079	0.83[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs1404213	0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs1477160	1.00[MEX][hapmap]
rs1477163	0.85[YRI][hapmap]
rs1543987	1.00[MEX][hapmap]
rs1861728	0.85[YRI][hapmap];0.91[AFR][1000 genomes]
rs1861730	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs1968198	0.85[YRI][hapmap]
rs1968199	0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.85[YRI][hapmap]
rs1974716	0.90[AFR][1000 genomes]
rs2041949	0.83[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs2140621	1.00[MEX][hapmap]
rs2177550	1.00[MEX][hapmap]
rs2193418	0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs28881872	1.00[MEX][hapmap]
rs2898638	1.00[MEX][hapmap]
rs3181009	0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap]
rs3800939	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs4576360	1.00[MEX][hapmap]
rs4727558	1.00[MEX][hapmap]
rs4727561	1.00[MEX][hapmap]
rs4729868	0.91[AFR][1000 genomes]
rs4729870	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs4729871	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs4729872	0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs4729874	0.87[AFR][1000 genomes]
rs4729877	0.81[AFR][1000 genomes]
rs4729878	0.91[AFR][1000 genomes]
rs4729882	0.85[YRI][hapmap]
rs59099783	0.94[EUR][1000 genomes]
rs60545001	0.94[EUR][1000 genomes]
rs61749912	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465883	1.00[MEX][hapmap]
rs6465884	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6465888	1.00[MEX][hapmap]
rs6465898	0.85[YRI][hapmap]
rs6465911	1.00[MEX][hapmap]
rs6946968	0.85[YRI][hapmap]
rs6946989	0.91[AFR][1000 genomes]
rs6950177	0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap]
rs6958533	1.00[MEX][hapmap]
rs6966872	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs6966961	0.85[YRI][hapmap]
rs6973702	1.00[MEX][hapmap]
rs6976034	0.85[YRI][hapmap]
rs6976794	0.85[YRI][hapmap]
rs6977206	1.00[MEX][hapmap]
rs7341515	1.00[MEX][hapmap]
rs7349957	0.90[AFR][1000 genomes]
rs7350051	0.91[AFR][1000 genomes]
rs7455410	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783856	0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap]
rs7784337	0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap]
rs7792240	0.85[YRI][hapmap]
rs7798381	0.94[EUR][1000 genomes]
rs7805950	1.00[MEX][hapmap]
rs7806136	1.00[MEX][hapmap]
rs7806691	1.00[MEX][hapmap]
rs7809075	1.00[MEX][hapmap]
rs847650	1.00[MEX][hapmap]
rs847653	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv526764	chr7:102701826-102737251	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6465890	SVH	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102716400-102723600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:102716400-102734000	Weak transcription	Esophagus	oesophagus
3	chr7:102716400-102745400	Weak transcription	Spleen	Spleen
4	chr7:102716600-102717800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:102716600-102717800	Enhancers	Fetal Muscle Leg	muscle
6	chr7:102716600-102718000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr7:102716600-102718600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr7:102716600-102721400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:102716600-102723600	Weak transcription	Placenta	Placenta
10	chr7:102716600-102724600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:102716600-102725000	Weak transcription	Left Ventricle	heart
12	chr7:102716600-102725000	Weak transcription	Ovary	ovary
13	chr7:102716600-102725400	Weak transcription	Aorta	Aorta
14	chr7:102716600-102735600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:102716600-102737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:102716600-102746400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:102716600-102746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:102716600-102746800	Weak transcription	Right Atrium	heart
19	chr7:102716600-102760200	Weak transcription	Lung	lung
20	chr7:102716600-102762200	Weak transcription	Colonic Mucosa	Colon
21	chr7:102716600-102768200	Weak transcription	Right Ventricle	heart
22	chr7:102716800-102717800	Enhancers	Primary B cells from cord blood	blood
23	chr7:102716800-102717800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:102716800-102718000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr7:102716800-102718000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:102716800-102718000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:102716800-102718000	Enhancers	Liver	Liver
28	chr7:102716800-102718200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:102716800-102718600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr7:102716800-102723800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:102716800-102724200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:102716800-102724600	Weak transcription	NHDF-Ad	bronchial
33	chr7:102716800-102725000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:102716800-102726400	Weak transcription	HSMMtube	muscle
35	chr7:102716800-102753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr7:102716800-102768400	Weak transcription	Stomach Mucosa	stomach
37	chr7:102717000-102717800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr7:102717000-102717800	Enhancers	Brain Substantia Nigra	brain
39	chr7:102717000-102717800	Enhancers	Hela-S3	cervix
40	chr7:102717000-102717800	Enhancers	HepG2	liver
41	chr7:102717000-102718000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:102717000-102718000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:102717000-102718000	Weak transcription	Colon Smooth Muscle	Colon
44	chr7:102717000-102718000	Enhancers	Fetal Brain Female	brain
45	chr7:102717000-102718200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr7:102717000-102718200	Enhancers	Brain Angular Gyrus	brain
47	chr7:102717000-102718200	Enhancers	Brain Anterior Caudate	brain
48	chr7:102717000-102718200	Enhancers	Brain Hippocampus Middle	brain
49	chr7:102717000-102718600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr7:102717000-102718800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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