Variant report

Variant	rs2422
Chromosome Location	chr12:120565188-120565189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120565131..120567860-chr12:120728248..120730165,2	K562	blood:
2	chr12:120563247..120566138-chr12:120667553..120669800,2	MCF-7	breast:
3	chr12:120565149..120566819-chr12:120568188..120570329,2	K562	blood:
4	chr12:120559989..120562800-chr12:120564491..120566220,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10744748	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10744749	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065028	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11065035	0.86[JPT][hapmap]
rs11065036	0.86[JPT][hapmap]
rs1151837	0.81[JPT][hapmap]
rs1183781	0.84[JPT][hapmap]
rs12310433	0.86[JPT][hapmap]
rs12312562	0.86[JPT][hapmap]
rs2074540	0.86[JPT][hapmap]
rs2238155	0.81[JPT][hapmap]
rs2240312	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2240317	0.86[JPT][hapmap]
rs2240318	0.86[JPT][hapmap]
rs2240321	0.86[JPT][hapmap]
rs2240322	0.86[JPT][hapmap]
rs2240323	0.86[JPT][hapmap]
rs2240325	0.81[JPT][hapmap]
rs2269941	0.86[JPT][hapmap]
rs2269944	0.86[JPT][hapmap]
rs2269945	0.86[JPT][hapmap]
rs2283362	0.81[JPT][hapmap]
rs2283364	0.81[JPT][hapmap]
rs2286049	0.86[JPT][hapmap]
rs2286050	0.86[JPT][hapmap]
rs2286051	0.86[JPT][hapmap]
rs3742039	0.86[JPT][hapmap]
rs3888586	0.81[JPT][hapmap]
rs7134706	0.86[JPT][hapmap]
rs7296380	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active 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	99 gene(s)	inside rSNPs	diseases
3	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
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2422	HCN1	trans	parietal	SCAN
rs2422	NME2P1	cis	cerebellum	SCAN
rs2422	GCN1L1	cis	multi-tissue	Pritchard
rs2422	ENSG00000089154	cis	multi-tissue	Pritchard
rs2422	GCN1L1	cis	parietal	SCAN
rs2422	SRSF9	cis	parietal	SCAN
rs2422	GCN1L1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120556800-120565200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:120556800-120567000	Weak transcription	Fetal Lung	lung
3	chr12:120556800-120571800	Weak transcription	Fetal Brain Male	brain
4	chr12:120556800-120578200	Weak transcription	Fetal Heart	heart
5	chr12:120557000-120565200	Weak transcription	Psoas Muscle	Psoas
6	chr12:120557600-120565200	Weak transcription	Small Intestine	intestine
7	chr12:120558000-120565200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:120560000-120565600	Weak transcription	Colonic Mucosa	Colon
9	chr12:120560400-120565200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:120562000-120567400	Weak transcription	Fetal Kidney	kidney
11	chr12:120562200-120567000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:120562400-120565200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:120562400-120567600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:120563000-120565400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:120563000-120568600	Strong transcription	Gastric	stomach
16	chr12:120563000-120580200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:120563000-120580200	Strong transcription	A549	lung
18	chr12:120563000-120588000	Strong transcription	HSMM	muscle
19	chr12:120563000-120596800	Strong transcription	Stomach Smooth Muscle	stomach
20	chr12:120563000-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:120563000-120629800	Strong transcription	Fetal Stomach	stomach
22	chr12:120563000-120630200	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:120563200-120565800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:120563200-120565800	Genic enhancers	NH-A	brain
25	chr12:120563200-120565800	Strong transcription	NHLF	lung
26	chr12:120563200-120602800	Strong transcription	Brain Germinal Matrix	brain
27	chr12:120563200-120630400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:120563400-120565200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:120563400-120565400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:120563400-120565600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:120563400-120570400	Strong transcription	Fetal Intestine Large	intestine
32	chr12:120563400-120616200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:120563400-120629200	Strong transcription	Fetal Intestine Small	intestine
34	chr12:120563400-120630200	Strong transcription	Fetal Thymus	thymus
35	chr12:120563600-120565400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:120563600-120565400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:120563600-120565400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr12:120563600-120565600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:120563600-120565600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:120563600-120565800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:120563600-120565800	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr12:120563600-120566000	Genic enhancers	HUVEC	blood vessel
43	chr12:120563600-120574600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:120563600-120580400	Strong transcription	Pancreas	Pancrea
45	chr12:120563600-120583600	Strong transcription	Fetal Brain Female	brain
46	chr12:120563600-120596400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:120563600-120602400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:120563600-120603600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:120563600-120603800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:120563600-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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