Variant report

Variant	rs2071836
Chromosome Location	chr6:13638243-13638244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13636958..13639286-chr6:13678817..13681067,2	K562	blood:
2	chr6:13621845..13624012-chr6:13637610..13640298,2	MCF-7	breast:
3	chr6:13613832..13619754-chr6:13637081..13641354,6	K562	blood:
4	chr6:13635435..13638835-chr6:13664717..13667757,3	K562	blood:
5	chr6:13633895..13638597-chr6:13710171..13713051,5	MCF-7	breast:
6	chr6:13636739..13638994-chr6:13648815..13651482,2	K562	blood:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000252966	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10484251	0.84[CHB][hapmap]
rs10948811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753232	0.84[CHB][hapmap]
rs11755634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11759518	0.84[CHB][hapmap]
rs11970591	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362519	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1362520	0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1573702	0.92[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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2080415	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237092	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299026	0.82[CHB][hapmap]
rs2299027	0.84[CHB][hapmap]
rs3846912	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3906327	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]
rs4715455	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715512	0.84[CHB][hapmap]
rs59120082	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459003	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459020	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[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]
rs6459025	0.93[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915775	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]
rs6940759	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72829117	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72831038	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7741241	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744218	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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475276	0.83[CHB][hapmap]

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
rs2071836	RANBP9	cis	cerebellum	SCAN
rs2071836	SIRT5	cis	cerebellum	SCAN
rs2071836	CAP2	cis	parietal	SCAN
rs2071836	HIVEP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13617200-13638800	Weak transcription	Aorta	Aorta
2	chr6:13617600-13642200	Strong transcription	Fetal Thymus	thymus
3	chr6:13617600-13642200	Strong transcription	HSMM	muscle
4	chr6:13617600-13642400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:13617800-13638400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:13618000-13641200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:13618000-13644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:13618200-13641800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:13618200-13644400	Strong transcription	K562	blood
10	chr6:13618200-13661200	Weak transcription	Fetal Brain Male	brain
11	chr6:13620000-13647200	Strong transcription	Dnd41	blood
12	chr6:13620000-13649600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:13620400-13660400	Weak transcription	Pancreas	Pancrea
14	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:13622200-13641600	Weak transcription	Right Ventricle	heart
16	chr6:13622800-13638800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:13622800-13640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:13623600-13656200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:13625200-13638400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:13625200-13638600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:13625200-13638600	Weak transcription	Fetal Intestine Small	intestine
22	chr6:13625400-13660400	Weak transcription	Gastric	stomach
23	chr6:13625600-13642600	Weak transcription	A549	lung
24	chr6:13626000-13660400	Weak transcription	Lung	lung
25	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
27	chr6:13630400-13638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:13631000-13642600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:13632000-13660400	Weak transcription	Psoas Muscle	Psoas
30	chr6:13632200-13638400	Weak transcription	Fetal Kidney	kidney
31	chr6:13632200-13641400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:13632600-13656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:13632800-13638400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:13632800-13638400	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:13632800-13638400	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:13632800-13638600	Weak transcription	Fetal Stomach	stomach
37	chr6:13632800-13638600	Weak transcription	Thymus	Thymus
38	chr6:13632800-13638800	Weak transcription	Esophagus	oesophagus
39	chr6:13632800-13645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:13632800-13653800	Weak transcription	Hela-S3	cervix
41	chr6:13633000-13640800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:13633800-13639000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr6:13634000-13644600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:13634200-13642000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:13634400-13641400	Strong transcription	Liver	Liver
46	chr6:13635200-13638600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:13635200-13639000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr6:13635600-13640400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:13635800-13641000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr6:13636000-13639400	Enhancers	Primary monocytes fromperipheralblood	blood

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