Variant report

Variant	rs6915775
Chromosome Location	chr6:13639700-13639701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13621845..13624012-chr6:13637610..13640298,2	MCF-7	breast:
2	chr6:13613832..13619754-chr6:13637081..13641354,6	K562	blood:
3	chr6:13614016..13617291-chr6:13638337..13642167,4	K562	blood:
4	chr6:13619203..13621025-chr6:13638291..13640853,2	K562	blood:
5	chr6:13638375..13640882-chr6:13640960..13643091,4	K562	blood:

Variant related genes	Relation type
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10807467	0.85[YRI][hapmap]
rs10948804	0.89[YRI][hapmap]
rs10948811	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755634	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11962124	0.85[YRI][hapmap]
rs11970591	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1362519	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1362520	0.88[CEU][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1573702	0.81[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071836	0.87[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080415	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2237092	0.81[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2841514	0.82[YRI][hapmap]
rs2841517	0.82[YRI][hapmap]
rs3757260	0.85[YRI][hapmap]
rs3800503	0.85[YRI][hapmap]
rs3846912	0.81[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3906327	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]
rs4715455	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59120082	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458997	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459003	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459020	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[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]
rs6459025	0.81[ASW][hapmap];0.84[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6899402	0.89[YRI][hapmap]
rs6911121	0.87[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940759	0.85[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72829117	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72831038	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741241	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7744218	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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6915775	HIVEP1	cis	parietal	SCAN
rs6915775	SIRT5	cis	cerebellum	SCAN
rs6915775	RANBP9	cis	cerebellum	SCAN
rs6915775	CAP2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13617600-13642200	Strong transcription	Fetal Thymus	thymus
2	chr6:13617600-13642200	Strong transcription	HSMM	muscle
3	chr6:13617600-13642400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:13618000-13641200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:13618000-13644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:13618200-13641800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:13618200-13644400	Strong transcription	K562	blood
8	chr6:13618200-13661200	Weak transcription	Fetal Brain Male	brain
9	chr6:13620000-13647200	Strong transcription	Dnd41	blood
10	chr6:13620000-13649600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:13620400-13660400	Weak transcription	Pancreas	Pancrea
12	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:13622200-13641600	Weak transcription	Right Ventricle	heart
14	chr6:13622800-13640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:13623600-13656200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:13625400-13660400	Weak transcription	Gastric	stomach
17	chr6:13625600-13642600	Weak transcription	A549	lung
18	chr6:13626000-13660400	Weak transcription	Lung	lung
19	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:13631000-13642600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:13632000-13660400	Weak transcription	Psoas Muscle	Psoas
23	chr6:13632200-13641400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:13632600-13656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:13632800-13645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:13632800-13653800	Weak transcription	Hela-S3	cervix
27	chr6:13633000-13640800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:13634000-13644600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr6:13634200-13642000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:13634400-13641400	Strong transcription	Liver	Liver
31	chr6:13635600-13640400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr6:13635800-13641000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr6:13636200-13639800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:13636400-13641000	Strong transcription	NHDF-Ad	bronchial
35	chr6:13636400-13641600	Strong transcription	Adipose Nuclei	Adipose
36	chr6:13636400-13645000	Strong transcription	Placenta	Placenta
37	chr6:13636600-13640000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:13636800-13652800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:13637200-13640000	Strong transcription	Primary B cells from cord blood	blood
40	chr6:13637200-13640400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:13637200-13640800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr6:13637200-13641000	Strong transcription	Fetal Lung	lung
43	chr6:13637200-13641200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:13637200-13642200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:13637200-13642400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:13637200-13650600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:13637400-13640000	Strong transcription	Fetal Intestine Large	intestine
48	chr6:13637400-13640000	Strong transcription	NHEK	skin
49	chr6:13637400-13640400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr6:13637400-13644000	Strong transcription	Rectal Mucosa Donor 29	rectum

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