Variant report

Variant	rs1634815
Chromosome Location	chr12:120687080-120687081
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120687079-120688316	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:120686890-120688841	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr12:120684586-120688694	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
2	chr12:120684888..120687057-chr12:120687063..120691406,4	MCF-7	breast:
3	chr12:120684404..120691478-chr12:120697984..120705218,14	MCF-7	breast:
4	chr12:120685214..120692467-chr12:120727115..120732311,17	K562	blood:
5	chr12:120685626..120692224-chr12:120727115..120732105,16	K562	blood:
6	chr12:120686832..120689716-chr12:120699360..120703521,4	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000089159	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000240925	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10849739	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11065061	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11065064	0.96[EUR][1000 genomes]
rs1151824	1.00[CEU][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151825	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151827	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1151832	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151837	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182859	0.83[ASN][1000 genomes]
rs1182860	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11831552	0.98[EUR][1000 genomes]
rs1183781	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164847	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12305146	0.95[EUR][1000 genomes]
rs12308431	0.85[EUR][1000 genomes]
rs12321884	0.86[ASN][1000 genomes]
rs12581983	0.91[ASN][1000 genomes]
rs1634814	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2006194	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2238155	0.81[ASN][1000 genomes]
rs2238156	0.98[EUR][1000 genomes]
rs2238157	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2239208	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2283362	0.88[ASN][1000 genomes]
rs2283364	0.83[CEU][hapmap];0.86[ASN][1000 genomes]
rs2283365	0.99[EUR][1000 genomes]
rs2524391	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759397	0.98[EUR][1000 genomes]
rs3888586	0.82[ASN][1000 genomes]
rs3888587	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3888588	0.99[EUR][1000 genomes]
rs3890165	0.98[EUR][1000 genomes]
rs3956833	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs4767886	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs61198412	0.98[EUR][1000 genomes]
rs7300273	0.98[EUR][1000 genomes]
rs739809	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7953949	0.98[EUR][1000 genomes]
rs7966099	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS 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	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120665200-120692000	Enhancers	Placenta	Placenta
2	chr12:120669800-120687600	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr12:120674200-120687600	Weak transcription	Fetal Kidney	kidney
4	chr12:120676400-120687400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:120676400-120699400	Weak transcription	Aorta	Aorta
6	chr12:120678800-120687200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:120679600-120687200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:120680200-120687400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:120680400-120687400	Weak transcription	Fetal Thymus	thymus
10	chr12:120681000-120687200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:120682000-120689000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:120682800-120687800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:120683000-120687200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:120683200-120687200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:120683200-120687200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:120683200-120687200	Weak transcription	Ovary	ovary
17	chr12:120683200-120687400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:120683200-120687400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:120683200-120687600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:120683200-120687600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:120683200-120694800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:120683200-120695200	Weak transcription	Fetal Brain Male	brain
23	chr12:120684000-120692000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:120684600-120687800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:120684600-120687800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:120684600-120688400	Enhancers	Pancreas	Pancrea
27	chr12:120684600-120690600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:120684800-120688200	Enhancers	Fetal Muscle Trunk	muscle
29	chr12:120684800-120688600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:120685000-120687200	Enhancers	Colon Smooth Muscle	Colon
31	chr12:120685000-120687200	Enhancers	Right Ventricle	heart
32	chr12:120685000-120687800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:120685000-120688400	Enhancers	Brain Hippocampus Middle	brain
34	chr12:120685000-120688600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:120685000-120688600	Enhancers	Fetal Heart	heart
36	chr12:120685000-120688800	Genic enhancers	Fetal Intestine Small	intestine
37	chr12:120685000-120690600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:120685200-120688400	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:120685200-120688600	Genic enhancers	Hela-S3	cervix
40	chr12:120685200-120688800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:120685200-120689000	Enhancers	K562	blood
42	chr12:120685400-120687200	Weak transcription	Stomach Mucosa	stomach
43	chr12:120685400-120688400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr12:120685400-120688400	Enhancers	Esophagus	oesophagus
45	chr12:120685400-120689600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr12:120685400-120690400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:120685400-120691200	Enhancers	Spleen	Spleen
48	chr12:120685600-120687200	Bivalent Enhancer	Primary B cells from cord blood	blood
49	chr12:120685600-120687800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr12:120685800-120687400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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