Variant report

Variant	rs9296240
Chromosome Location	chr6:38210519-38210520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38210095..38212639-chr6:38215015..38217311,2	K562	blood:
2	chr6:38210257..38213113-chr6:38213804..38216436,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055689	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055699	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12176364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60235041	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7356828	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356904	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745176	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755820	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756174	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756345	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756480	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs915161	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs926564	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9296239	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349060	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349061	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349062	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349063	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366950	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9369040	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369041	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462417	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs9470832	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv969296	chr6:38210477-38213915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:38186600-38215200	Weak transcription	Aorta	Aorta
5	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:38203400-38212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:38204200-38215200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:38204800-38229400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:38205200-38211000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:38205200-38216200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:38205200-38228800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:38207800-38229400	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:38208000-38212600	Weak transcription	Right Ventricle	heart
14	chr6:38208000-38213000	Weak transcription	Left Ventricle	heart
15	chr6:38208000-38221600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:38208000-38222400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:38208000-38226400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:38208200-38211000	Weak transcription	Stomach Mucosa	stomach
19	chr6:38208200-38212800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:38208200-38213000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:38208200-38213000	Weak transcription	Lung	lung
22	chr6:38208200-38213000	Weak transcription	Right Atrium	heart
23	chr6:38208200-38215200	Weak transcription	Pancreas	Pancrea
24	chr6:38208200-38216400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:38208200-38216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:38208200-38216400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:38208200-38222200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:38208200-38226000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:38208200-38227600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:38208200-38236600	Weak transcription	Gastric	stomach
31	chr6:38208200-38255000	Weak transcription	Ovary	ovary
32	chr6:38208600-38222400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:38209000-38229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:38209200-38210800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:38209200-38210800	Strong transcription	Primary B cells from cord blood	blood
36	chr6:38209200-38227000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:38209600-38221000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:38209800-38212600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:38210400-38210800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:38210400-38213000	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links