Variant report

Variant	rs12635956
Chromosome Location	chr3:120315852-120315853
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:120314753-120315872	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:120314752-120316829	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:120314603-120316861	K562	blood:	n/a	n/a
4	REST	chr3:120314499-120316047	H1-neurons	neurons:	n/a	chr3:120315125-120315145
5	POLR2A	chr3:120314614-120317060	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:120314571-120316834	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:120315040..120318401-chr3:120459431..120463263,5	MCF-7	breast:
2	chr3:120313507..120317684-chr3:120458763..120463692,6	MCF-7	breast:
3	chr3:120066931..120069030-chr3:120314504..120317461,2	MCF-7	breast:

Variant related genes	Relation type
NDUFB4	TF binding region
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1465837	0.87[AMR][1000 genomes]
rs1583654	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831523	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17140281	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17140284	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34438738	0.86[AMR][1000 genomes]
rs34924588	0.86[AMR][1000 genomes]
rs35085316	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72625410	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72625411	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72625413	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72625414	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72625415	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72625416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7626272	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv508238	chr3:120248574-120329424	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
12	esv3427031	chr3:120314687-120317235	Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120314200-120316000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:120314400-120316000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:120314400-120316000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:120314400-120316000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:120314400-120316000	Active TSS	K562	blood
6	chr3:120314400-120316200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:120314400-120317000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:120314600-120316000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:120314600-120316000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:120314600-120316000	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr3:120314600-120316000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:120314600-120316000	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:120314600-120316000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:120314600-120316000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:120314600-120316000	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr3:120314600-120316000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:120314600-120316000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:120314600-120316000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:120314600-120316000	Active TSS	Liver	Liver
20	chr3:120314600-120316000	Active TSS	Brain Angular Gyrus	brain
21	chr3:120314600-120316000	Active TSS	Brain Anterior Caudate	brain
22	chr3:120314600-120316000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:120314600-120316000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:120314600-120316000	Active TSS	Colonic Mucosa	Colon
25	chr3:120314600-120316000	Active TSS	Colon Smooth Muscle	Colon
26	chr3:120314600-120316000	Active TSS	Fetal Brain Female	brain
27	chr3:120314600-120316000	Active TSS	Fetal Intestine Large	intestine
28	chr3:120314600-120316000	Active TSS	Fetal Intestine Small	intestine
29	chr3:120314600-120316000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:120314600-120316000	Active TSS	Fetal Muscle Leg	muscle
31	chr3:120314600-120316000	Active TSS	Fetal Stomach	stomach
32	chr3:120314600-120316000	Active TSS	Fetal Thymus	thymus
33	chr3:120314600-120316000	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr3:120314600-120316000	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:120314600-120316000	Active TSS	Thymus	Thymus
36	chr3:120314600-120316000	Active TSS	HSMM	muscle
37	chr3:120314600-120316000	Active TSS	HSMMtube	muscle
38	chr3:120314600-120316000	Active TSS	HUVEC	blood vessel
39	chr3:120314600-120316000	Active TSS	NHLF	lung
40	chr3:120314600-120316200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:120314600-120316200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:120314600-120316200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:120314600-120316200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:120314600-120316200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:120314600-120316200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:120314600-120316200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:120314600-120316200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:120314600-120316200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:120314600-120316200	Active TSS	Aorta	Aorta
50	chr3:120314600-120316200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links