Variant report

Variant	rs12693378
Chromosome Location	chr2:153348605-153348606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153333966..153336557-chr2:153346831..153349647,2	MCF-7	breast:
2	chr2:153345928..153348906-chr2:153354040..153356962,2	MCF-7	breast:
3	chr2:153344407..153345927-chr2:153347913..153350006,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10173398	0.83[CEU][hapmap]
rs10173899	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10179418	0.94[JPT][hapmap]
rs10194603	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10208776	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10432493	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11892232	0.83[CEU][hapmap]
rs12616906	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13390698	0.94[JPT][hapmap]
rs13424038	1.00[JPT][hapmap]
rs13427076	0.94[JPT][hapmap]
rs13427990	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831169	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16831174	1.00[JPT][hapmap]
rs2078444	0.92[ASN][1000 genomes]
rs2346205	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2346209	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2881339	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4143274	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4146259	0.89[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4664112	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4664587	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4664589	0.81[ASN][1000 genomes]
rs4664590	0.81[ASN][1000 genomes]
rs59965317	0.87[ASN][1000 genomes]
rs6434059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434060	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434061	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434062	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725661	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6737699	0.94[JPT][hapmap]
rs6747765	0.94[JPT][hapmap]
rs6748954	1.00[JPT][hapmap]
rs73968029	0.81[ASN][1000 genomes]
rs7559217	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7582984	1.00[JPT][hapmap]
rs7586195	1.00[JPT][hapmap]
rs7587794	1.00[JPT][hapmap]
rs7590207	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7592283	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7606592	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2830258	chr2:153318339-153349165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153334400-153353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:153338600-153353400	Weak transcription	NHEK	skin
3	chr2:153340600-153354200	Weak transcription	Small Intestine	intestine
4	chr2:153342000-153349000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:153342000-153351600	Enhancers	Brain Substantia Nigra	brain
6	chr2:153342000-153351800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:153342400-153350000	Weak transcription	Right Ventricle	heart
8	chr2:153342600-153355800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:153343000-153360600	Enhancers	Brain Anterior Caudate	brain
10	chr2:153343200-153350000	Weak transcription	HUVEC	blood vessel
11	chr2:153343800-153349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:153344800-153351000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:153345000-153351600	Enhancers	Fetal Lung	lung
14	chr2:153345200-153348800	Enhancers	Fetal Stomach	stomach
15	chr2:153345200-153349000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:153345400-153351400	Enhancers	Brain Angular Gyrus	brain
17	chr2:153345600-153348800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:153345600-153349400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:153345600-153349600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr2:153345600-153350800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:153345800-153350000	Weak transcription	Gastric	stomach
22	chr2:153345800-153351600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:153346000-153349400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:153346200-153349800	Weak transcription	A549	lung
25	chr2:153346200-153350000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:153346200-153350000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:153346200-153352800	Weak transcription	GM12878-XiMat	blood
28	chr2:153346400-153348800	Enhancers	Fetal Intestine Small	intestine
29	chr2:153346400-153348800	Enhancers	Ovary	ovary
30	chr2:153346600-153350000	Enhancers	NHDF-Ad	bronchial
31	chr2:153346600-153351400	Enhancers	Adipose Nuclei	Adipose
32	chr2:153346800-153349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:153346800-153349400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:153347000-153348800	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:153347400-153349200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:153347600-153349000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:153347600-153349400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:153347600-153354200	Weak transcription	Pancreas	Pancrea
39	chr2:153347800-153349000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:153347800-153350000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:153347800-153351000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:153347800-153351800	Enhancers	Brain Hippocampus Middle	brain
43	chr2:153347800-153354400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:153348000-153349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:153348000-153349400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:153348000-153350000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:153348000-153350000	Weak transcription	Psoas Muscle	Psoas
48	chr2:153348000-153350000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:153348000-153350600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:153348000-153350600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links