Variant report

Variant	rs2596144
Chromosome Location	chr12:122297738-122297739
allele	C/T
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	JUND	chr12:122297083-122297774	T-47D	breast:	n/a	chr12:122297450-122297461
2	JUND	chr12:122297067-122297761	T-47D	breast:	n/a	chr12:122297450-122297461
3	GATA3	chr12:122296655-122297762	SK-N-SH	brain:	n/a	n/a
4	JUND	chr12:122297024-122297788	HCT-116	colon:	n/a	chr12:122297450-122297461
5	POLR2A	chr12:122297592-122298021	HepG2	liver:	n/a	n/a
6	EP300	chr12:122297007-122297759	SK-N-SH	brain:	n/a	n/a
7	JUND	chr12:122296416-122297837	SK-N-SH	brain:	n/a	chr12:122297450-122297461

No.	Distal block	Cell Line	Cell type
1	chr12:122237722..122239509-chr12:122297633..122299963,2	MCF-7	breast:
2	chr12:122293214..122297138-chr12:122297451..122299741,3	K562	blood:
3	chr12:122297229..122298765-chr12:122371936..122374229,2	K562	blood:
4	chr12:122231575..122234439-chr12:122297036..122301100,4	MCF-7	breast:

Variant related genes	Relation type
HPD	TF binding region
ENSG00000139725	Chromatin interaction
ENSG00000256811	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000158104	Chromatin interaction
ENSG00000212694	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10840626	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840627	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11043222	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11043226	0.87[AMR][1000 genomes]
rs11502392	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1154510	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154515	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11614623	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1169077	0.82[CEU][hapmap]
rs1169085	0.82[CEU][hapmap]
rs1169093	0.82[CEU][hapmap]
rs1182927	0.82[CEU][hapmap]
rs1185260	1.00[CEU][hapmap];0.95[TSI][hapmap]
rs1667580	0.81[EUR][1000 genomes]
rs1667583	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1678967	0.86[AMR][1000 genomes]
rs1678969	0.84[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1720041	0.82[CEU][hapmap]
rs1720067	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1795963	0.83[ASN][1000 genomes]
rs1795967	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1947826	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2101017	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2230681	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247139	0.81[EUR][1000 genomes]
rs2247291	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309274	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2596137	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2620332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2620340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688412	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2707056	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2707075	0.98[ASN][1000 genomes]
rs4760099	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs493519	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs6486794	0.82[CEU][hapmap]
rs7314056	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957207	0.91[CEU][hapmap]
rs7961103	0.91[CEU][hapmap]
rs830122	0.82[CEU][hapmap]
rs830124	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs853758	1.00[CEU][hapmap]
rs895958	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs895959	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9668191	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2596144	RNF10	cis	cerebellum	SCAN
rs2596144	CCDC62	cis	parietal	SCAN
rs2596144	SETD1B	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122294000-122298600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:122294200-122297800	Weak transcription	Primary B cells from cord blood	blood
3	chr12:122294200-122299000	Enhancers	A549	lung
4	chr12:122294600-122297800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:122294800-122298800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:122295200-122298600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:122295400-122297800	Enhancers	Fetal Intestine Small	intestine
8	chr12:122295400-122300000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:122295400-122300400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:122295600-122298000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:122295600-122298400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:122295600-122298400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:122295600-122298400	Enhancers	Adipose Nuclei	Adipose
14	chr12:122295600-122298600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:122295600-122298600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:122295800-122299200	Weak transcription	K562	blood
17	chr12:122296200-122298000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:122296200-122298400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:122296200-122298800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:122296400-122297800	Enhancers	Colonic Mucosa	Colon
21	chr12:122296400-122297800	Enhancers	Fetal Muscle Leg	muscle
22	chr12:122296400-122297800	Enhancers	Fetal Stomach	stomach
23	chr12:122296400-122297800	Enhancers	Ovary	ovary
24	chr12:122296400-122297800	Enhancers	Right Ventricle	heart
25	chr12:122296400-122297800	Enhancers	HSMM	muscle
26	chr12:122296400-122297800	Enhancers	HSMMtube	muscle
27	chr12:122296400-122298000	Enhancers	NHLF	lung
28	chr12:122296400-122298400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:122296400-122298400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:122296400-122298600	Enhancers	Right Atrium	heart
31	chr12:122296400-122298600	Enhancers	Hela-S3	cervix
32	chr12:122296600-122297800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:122296600-122297800	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr12:122296600-122298000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:122296600-122298400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:122296600-122298400	Enhancers	Left Ventricle	heart
37	chr12:122296600-122298400	Enhancers	HMEC	breast
38	chr12:122296600-122298800	Enhancers	Psoas Muscle	Psoas
39	chr12:122296800-122297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:122296800-122298400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:122296800-122298600	Flanking Active TSS	HepG2	liver
42	chr12:122297000-122298200	Weak transcription	Lung	lung
43	chr12:122297000-122304200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:122297200-122298000	Flanking Active TSS	Liver	Liver
45	chr12:122297200-122299600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:122297200-122299600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:122297200-122299800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:122297400-122297800	Weak transcription	Aorta	Aorta
49	chr12:122297400-122297800	Weak transcription	Pancreas	Pancrea
50	chr12:122297400-122298400	Enhancers	HUES6 Cell Line	embryonic stem cell

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