Variant report

Variant	rs12612136
Chromosome Location	chr2:96895918-96895919
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96873650..96875657-chr2:96893233..96896003,2	MCF-7	breast:
2	chr2:96872852..96874704-chr2:96894176..96896197,2	K562	blood:
3	chr2:96874120..96876573-chr2:96894198..96895998,3	K562	blood:

Variant related genes	Relation type
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12611936	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12614113	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs12614623	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12616326	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619114	1.00[AMR][1000 genomes]
rs12619490	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619573	1.00[AMR][1000 genomes]
rs12619919	1.00[AMR][1000 genomes]
rs12620576	1.00[AMR][1000 genomes]
rs12620768	1.00[AMR][1000 genomes]
rs12621163	1.00[AMR][1000 genomes]
rs12621619	1.00[AMR][1000 genomes]
rs12621688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276647	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2290908	1.00[AMR][1000 genomes]
rs3813659	1.00[AMR][1000 genomes]
rs3813660	1.00[AMR][1000 genomes]
rs56742757	0.96[ASN][1000 genomes]
rs57213829	1.00[AMR][1000 genomes]
rs57248244	1.00[ASN][1000 genomes]
rs57319731	1.00[AMR][1000 genomes]
rs57367779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57477571	1.00[AMR][1000 genomes]
rs58132887	1.00[AMR][1000 genomes]
rs58152078	1.00[AMR][1000 genomes]
rs59168739	1.00[AMR][1000 genomes]
rs59525841	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59621486	1.00[AMR][1000 genomes]
rs59911784	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59939559	1.00[AMR][1000 genomes]
rs60013962	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60020980	1.00[AMR][1000 genomes]
rs60302421	1.00[AMR][1000 genomes]
rs60596893	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893927	1.00[AMR][1000 genomes]
rs61096003	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv963665	chr2:96882253-96905611	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96875000-96906200	Weak transcription	Esophagus	oesophagus
2	chr2:96875200-96905000	Weak transcription	Aorta	Aorta
3	chr2:96875600-96907000	Weak transcription	Fetal Thymus	thymus
4	chr2:96875800-96905800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:96876000-96896200	Weak transcription	Left Ventricle	heart
6	chr2:96876000-96902400	Weak transcription	Fetal Intestine Large	intestine
7	chr2:96876000-96904200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:96876000-96905800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:96876000-96906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:96876200-96903200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:96876200-96903600	Weak transcription	Gastric	stomach
13	chr2:96876200-96905200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:96876200-96906000	Weak transcription	Osteobl	bone
15	chr2:96876200-96906600	Weak transcription	Brain Anterior Caudate	brain
16	chr2:96876200-96916000	Weak transcription	Dnd41	blood
17	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:96876600-96902600	Weak transcription	HepG2	liver
19	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:96879600-96902400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:96879600-96903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:96879600-96903200	Weak transcription	Fetal Stomach	stomach
23	chr2:96886000-96905400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:96886000-96905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:96886400-96905000	Weak transcription	Fetal Heart	heart
26	chr2:96886800-96902200	Weak transcription	Fetal Intestine Small	intestine
27	chr2:96886800-96905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:96887800-96905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:96888000-96905400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:96888600-96896000	Weak transcription	Right Ventricle	heart
31	chr2:96889000-96903600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:96889600-96903400	Weak transcription	Primary T cells from cord blood	blood
33	chr2:96889600-96915800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:96891200-96916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:96891400-96896000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:96891400-96902200	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:96891400-96902800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:96891400-96916400	Weak transcription	HSMM	muscle
39	chr2:96891600-96896400	Weak transcription	K562	blood
40	chr2:96891600-96905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:96891600-96906800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:96891800-96899600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:96892000-96898800	Weak transcription	GM12878-XiMat	blood
44	chr2:96892200-96898600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr2:96892600-96898600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:96893200-96902400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:96893200-96907600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:96895600-96896200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:96895800-96896200	Enhancers	Pancreas	Pancrea
50	chr2:96895800-96896200	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links