Variant report

Variant	rs12153885
Chromosome Location	chr6:25424003-25424004
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12195837	0.96[ASN][1000 genomes]
rs12200019	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12206709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1304166	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[ASN][1000 genomes]
rs1876372	0.88[ASN][1000 genomes]
rs1876373	0.88[ASN][1000 genomes]
rs2076890	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905021	0.81[ASN][1000 genomes]
rs72831248	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831254	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7449710	0.88[ASN][1000 genomes]
rs7760659	0.96[ASN][1000 genomes]
rs9461171	0.88[ASN][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12153885	ZNF184	cis	cerebellum	SCAN
rs12153885	C6orf62	cis	cerebellum	SCAN
rs12153885	CMAH	cis	cerebellum	SCAN
rs12153885	HIST1H2AK	cis	parietal	SCAN
rs12153885	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs12153885	HIST1H2BC	cis	parietal	SCAN
rs12153885	HIST1H1T	cis	parietal	SCAN
rs12153885	PRL	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:25415200-25431800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
5	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
6	chr6:25416600-25427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:25417600-25431800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:25418000-25429200	Weak transcription	Aorta	Aorta
10	chr6:25418600-25426200	Weak transcription	Gastric	stomach
11	chr6:25418800-25462600	Weak transcription	Ovary	ovary
12	chr6:25419400-25430600	Weak transcription	Left Ventricle	heart
13	chr6:25419800-25429000	Weak transcription	Small Intestine	intestine
14	chr6:25420600-25425400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:25420600-25426200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:25420600-25429400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:25420600-25432000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:25420800-25431800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:25420800-25431800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:25420800-25436600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:25420800-25441800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:25420800-25445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:25421000-25431400	Weak transcription	Fetal Lung	lung
24	chr6:25421000-25431800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:25421000-25438600	Weak transcription	Primary B cells from cord blood	blood
26	chr6:25421000-25440400	Weak transcription	Primary T cells from cord blood	blood
27	chr6:25421400-25425200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:25421400-25425400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:25421400-25425600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:25421400-25429400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:25421400-25436400	Weak transcription	Fetal Intestine Large	intestine
32	chr6:25421400-25442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:25421400-25446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:25421600-25432000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:25421600-25446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25423200-25439800	Weak transcription	NHEK	skin
37	chr6:25423600-25424200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:25423600-25424800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:25423600-25425200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:25423800-25424800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:25423800-25425000	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:25424000-25424200	Enhancers	Thymus	Thymus
43	chr6:25424000-25426200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:25424000-25426600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:25424000-25429400	Weak transcription	Right Atrium	heart

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