Variant report

Variant	rs1653583
Chromosome Location	chr12:121598652-121598653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121593895..121595665-chr12:121598530..121600220,2	K562	blood:
2	chr12:121574197..121575819-chr12:121598623..121600574,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1169714	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12301635	0.82[CHB][hapmap]
rs12304035	0.82[CHB][hapmap]
rs12321707	0.82[CHB][hapmap]
rs12815078	0.82[CHB][hapmap]
rs1653584	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718125	0.92[TSI][hapmap]
rs1718149	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718162	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794886	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1794887	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051551	0.82[CHB][hapmap]
rs208288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs208310	0.82[CHB][hapmap]
rs2686369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686371	0.82[CHB][hapmap]
rs2857588	0.82[CHB][hapmap]
rs2857589	0.82[CHB][hapmap]
rs35646440	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs487417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs510660	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511496	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs535557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590477	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592340	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593223	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs594423	1.00[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608425	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622937	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657995	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs672140	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137837	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS 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	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
6	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121571800-121623200	Weak transcription	Colonic Mucosa	Colon
2	chr12:121572200-121599800	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:121572800-121601600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:121583000-121613200	Weak transcription	Primary B cells from cord blood	blood
5	chr12:121583000-121634600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:121583600-121599600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:121583800-121600400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:121583800-121602000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:121583800-121603200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:121583800-121623600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:121583800-121634400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:121584600-121626600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:121586200-121623600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:121592000-121599000	Strong transcription	Ovary	ovary
15	chr12:121594000-121612600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:121594200-121627600	Weak transcription	Right Ventricle	heart
17	chr12:121594400-121600000	Weak transcription	Spleen	Spleen
18	chr12:121594600-121605400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:121595200-121606200	Strong transcription	Brain Angular Gyrus	brain
20	chr12:121596000-121614800	Weak transcription	Gastric	stomach
21	chr12:121596200-121599800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:121596200-121601800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:121596200-121602800	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr12:121596200-121603200	Weak transcription	Adipose Nuclei	Adipose
25	chr12:121596200-121603200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:121596200-121622200	Weak transcription	Esophagus	oesophagus
27	chr12:121596200-121625600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:121596200-121629000	Weak transcription	Left Ventricle	heart
29	chr12:121596400-121600200	Weak transcription	Lung	lung
30	chr12:121596400-121603400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:121596400-121606800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:121596400-121609000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr12:121596400-121609400	Strong transcription	Brain Hippocampus Middle	brain
34	chr12:121596400-121610200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:121596400-121634200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:121597600-121598800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:121597600-121600400	Weak transcription	Pancreas	Pancrea
38	chr12:121597600-121603600	Weak transcription	Fetal Intestine Small	intestine
39	chr12:121597800-121598800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:121597800-121600000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:121597800-121601600	Weak transcription	Placenta	Placenta
42	chr12:121597800-121603000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:121597800-121606600	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:121597800-121625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:121598200-121599200	Strong transcription	Brain Anterior Caudate	brain
46	chr12:121598200-121604200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:121598400-121598800	Strong transcription	Primary T cells from cord blood	blood
48	chr12:121598400-121604800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:121598400-121605800	Strong transcription	Brain Substantia Nigra	brain
50	chr12:121598400-121606200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links