Variant report

Variant	rs2273921
Chromosome Location	chr6:57006933-57006934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57005871..57008219-chr6:57037080..57038650,2	K562	blood:
2	chr6:57002952..57005589-chr6:57005953..57008891,3	MCF-7	breast:
3	chr6:57005006..57007757-chr6:57049256..57051462,2	K562	blood:
4	chr6:57005624..57007757-chr6:57049962..57051684,2	K562	blood:

Variant related genes	Relation type
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1157713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190434	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192711	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210597	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12211611	0.89[CHB][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2100305	0.80[ASN][1000 genomes]
rs3734738	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800019	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs3996929	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996933	0.80[ASN][1000 genomes]
rs3996937	0.82[ASN][1000 genomes]
rs4715646	0.80[ASN][1000 genomes]
rs6459180	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913707	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926980	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928715	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929783	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743855	0.93[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7744316	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7744824	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753537	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753927	0.93[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs7763570	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180538	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349843	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367704	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9367708	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382680	0.88[YRI][hapmap]
rs9382689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396259	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952647	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885757	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2273921	BEND6	cis	cerebellum	SCAN
rs2273921	RAB23	cis	cerebellum	SCAN
rs2273921	KIAA1586	cis	cerebellum	SCAN
rs2273921	BEND6	cis	parietal	SCAN
rs2273921	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs2273921	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs2273921	ZNF451	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56966600-57012400	Weak transcription	Spleen	Spleen
2	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
5	chr6:56970200-57007600	Weak transcription	Fetal Kidney	kidney
6	chr6:56974000-57012400	Weak transcription	HUVEC	blood vessel
7	chr6:56974200-57012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
9	chr6:56986400-57012000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:56988000-57009000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:56988200-57009400	Weak transcription	Fetal Intestine Small	intestine
12	chr6:56991600-57036600	Weak transcription	Small Intestine	intestine
13	chr6:56993000-57017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:56994400-57012000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:56995600-57012000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:56995800-57008800	Weak transcription	Fetal Stomach	stomach
17	chr6:56995800-57012600	Weak transcription	Right Ventricle	heart
18	chr6:56995800-57036600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:56996000-57036800	Weak transcription	Gastric	stomach
20	chr6:56996200-57012200	Weak transcription	Lung	lung
21	chr6:56996200-57036600	Weak transcription	Fetal Brain Male	brain
22	chr6:56996400-57012200	Weak transcription	Fetal Heart	heart
23	chr6:56996400-57036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:56997000-57011800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:56997200-57012400	Weak transcription	Esophagus	oesophagus
26	chr6:56997400-57012000	Weak transcription	Colonic Mucosa	Colon
27	chr6:56998800-57027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:56999000-57011800	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:56999000-57012000	Weak transcription	Aorta	Aorta
30	chr6:56999000-57012000	Weak transcription	Ovary	ovary
31	chr6:56999600-57008400	Weak transcription	Fetal Brain Female	brain
32	chr6:56999600-57012000	Weak transcription	Left Ventricle	heart
33	chr6:56999800-57012000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:56999800-57012000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:56999800-57012400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:56999800-57036600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:57000000-57007000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:57000000-57008400	Weak transcription	GM12878-XiMat	blood
39	chr6:57000000-57011800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:57000200-57012000	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:57001200-57013000	Weak transcription	Hela-S3	cervix
42	chr6:57001200-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr6:57001800-57018600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:57002600-57007000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:57002600-57011800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:57002600-57012000	Weak transcription	Thymus	Thymus
47	chr6:57002600-57036600	Weak transcription	A549	lung
48	chr6:57002800-57012200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:57003000-57012400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:57003800-57009000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links