Variant report

Variant	rs3906327
Chromosome Location	chr6:13667769-13667770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13662528..13665439-chr6:13667609..13669664,2	MCF-7	breast:
2	chr6:13667308..13669773-chr6:13712805..13714594,2	K562	blood:
3	chr6:13658437..13687167-chr6:13707669..13717356,51	K562	blood:
4	chr6:13614409..13618371-chr6:13665029..13668940,4	K562	blood:
5	chr6:13657137..13658911-chr6:13667084..13669198,2	MCF-7	breast:
6	chr6:13664693..13668460-chr6:13708038..13711894,3	K562	blood:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10484251	0.84[CHB][hapmap]
rs10807467	0.93[YRI][hapmap]
rs10948804	0.96[YRI][hapmap]
rs10948811	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11753232	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs11755634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11759518	0.84[CHB][hapmap]
rs11962124	0.93[YRI][hapmap]
rs11970591	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362519	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1362520	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1573702	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071836	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080415	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237092	0.96[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2299026	0.82[CHB][hapmap]
rs2299027	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2841514	0.89[YRI][hapmap]
rs2841517	0.89[YRI][hapmap]
rs3757260	0.93[YRI][hapmap]
rs3800503	0.93[YRI][hapmap]
rs3846912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715455	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715512	0.84[CHB][hapmap]
rs59120082	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458997	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459003	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459025	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899402	0.89[YRI][hapmap]
rs6911121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915775	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940759	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72829117	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831038	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741241	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7744218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475276	0.83[CHB][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1026597	chr6:13634669-13689882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3906327	HIVEP1	cis	parietal	SCAN
rs3906327	RANBP9	cis	cerebellum	SCAN
rs3906327	SIRT5	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
4	chr6:13639800-13669800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:13652400-13669600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:13652600-13667800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:13652600-13669800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:13653000-13674600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:13654600-13689800	Weak transcription	Osteobl	bone
10	chr6:13655400-13677000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:13657000-13680200	Weak transcription	HSMM	muscle
12	chr6:13657600-13670400	Weak transcription	Dnd41	blood
13	chr6:13658800-13670200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:13659200-13670400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:13659600-13669000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr6:13659800-13670200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:13660000-13670000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:13660200-13670000	Enhancers	HepG2	liver
19	chr6:13660400-13669800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr6:13660400-13670000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:13660400-13670000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:13660800-13667800	Weak transcription	Ovary	ovary
23	chr6:13660800-13674800	Weak transcription	Lung	lung
24	chr6:13660800-13675400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:13660800-13688000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:13661400-13669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13661400-13669800	Weak transcription	Pancreas	Pancrea
28	chr6:13661600-13672800	Weak transcription	Brain Angular Gyrus	brain
29	chr6:13661600-13678600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:13662600-13669200	Enhancers	Hela-S3	cervix
31	chr6:13662600-13670200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:13663000-13669800	Weak transcription	Esophagus	oesophagus
33	chr6:13663000-13672200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:13663000-13674800	Weak transcription	Gastric	stomach
35	chr6:13663200-13669000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:13663200-13674800	Weak transcription	Aorta	Aorta
37	chr6:13663200-13678200	Weak transcription	Small Intestine	intestine
38	chr6:13663400-13668600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:13663400-13672200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:13663800-13668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:13663800-13668400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:13664200-13669400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:13664400-13669400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:13665000-13668000	Enhancers	Primary T cells from cord blood	blood
45	chr6:13665200-13667800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:13665400-13669600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:13665400-13670000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:13665600-13695200	Weak transcription	NHLF	lung
49	chr6:13665800-13672000	Weak transcription	Liver	Liver
50	chr6:13665800-13674800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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