Variant report

Variant	rs2533877
Chromosome Location	chr7:2882421-2882422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
2	chr7:2801788..2804432-chr7:2882018..2884117,3	K562	blood:
3	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231357	Chromatin interaction
ENSG00000146535	Chromatin interaction
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1182155	0.86[EUR][1000 genomes]
rs1182174	0.81[EUR][1000 genomes]
rs1182177	0.80[EUR][1000 genomes]
rs1182181	0.80[EUR][1000 genomes]
rs1182182	0.80[EUR][1000 genomes]
rs1182183	0.80[EUR][1000 genomes]
rs1182199	0.82[EUR][1000 genomes]
rs1183085	0.80[EUR][1000 genomes]
rs11973498	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12700373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230946	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13230995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1614791	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1636247	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636248	0.95[ASN][1000 genomes]
rs1636249	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636250	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636251	0.92[ASN][1000 genomes]
rs1636252	0.93[ASN][1000 genomes]
rs1636253	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636254	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636255	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1636256	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1636264	0.82[EUR][1000 genomes]
rs1639034	0.93[ASN][1000 genomes]
rs1639036	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639040	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1639066	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1713912	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1713921	0.96[ASN][1000 genomes]
rs2527677	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527680	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527681	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533871	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533875	0.94[ASN][1000 genomes]
rs2533878	0.82[EUR][1000 genomes]
rs2533889	0.82[EUR][1000 genomes]
rs2533891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644281	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644286	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644309	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679259	0.93[ASN][1000 genomes]
rs71522301	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71522302	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71524003	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7783400	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[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	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2533877	GNA12	cis	Artery Tibial	GTEx
rs2533877	GNA12	cis	multi-tissue	Pritchard
rs2533877	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2533877	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
2	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
3	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
5	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
6	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:2872600-2882800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:2872800-2882600	Weak transcription	Psoas Muscle	Psoas
9	chr7:2872800-2882800	Weak transcription	Liver	Liver
10	chr7:2874800-2882800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:2875000-2882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:2876200-2882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:2877400-2882800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:2877600-2882600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr7:2877600-2882600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:2877800-2882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:2878000-2882600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:2878000-2882800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:2878200-2882600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:2878200-2882800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:2878400-2882800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:2879000-2882600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:2879000-2882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:2879200-2882800	Weak transcription	Small Intestine	intestine
25	chr7:2879400-2882600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:2879800-2883400	Enhancers	Fetal Heart	heart
27	chr7:2880800-2882800	Enhancers	Left Ventricle	heart
28	chr7:2881000-2882800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr7:2881000-2883000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:2881000-2883000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
31	chr7:2881200-2882600	Enhancers	Rectal Smooth Muscle	rectum
32	chr7:2881200-2882800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr7:2881200-2882800	Enhancers	Pancreas	Pancrea
34	chr7:2881200-2882800	Enhancers	Right Ventricle	heart
35	chr7:2881200-2883400	Enhancers	Fetal Brain Male	brain
36	chr7:2881400-2882600	Genic enhancers	Fetal Intestine Small	intestine
37	chr7:2881400-2882600	Genic enhancers	Fetal Lung	lung
38	chr7:2881400-2882800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr7:2881400-2883000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr7:2881600-2882600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
41	chr7:2881600-2882600	Enhancers	Brain Substantia Nigra	brain
42	chr7:2881600-2882800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:2881600-2883200	Enhancers	Spleen	Spleen
44	chr7:2881800-2882600	Genic enhancers	Fetal Stomach	stomach
45	chr7:2881800-2882600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr7:2881800-2882600	Genic enhancers	GM12878-XiMat	blood
47	chr7:2881800-2882800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:2881800-2882800	Enhancers	Fetal Thymus	thymus
49	chr7:2881800-2882800	Enhancers	Lung	lung
50	chr7:2881800-2882800	Genic enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links