Variant report

Variant	rs6433738
Chromosome Location	chr2:179710706-179710707
allele	A/G
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	NFIC	chr2:179710163-179710820	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:179710510-179710995	H1-neurons	neurons:	n/a	n/a
3	GATA3	chr2:179710090-179710836	SK-N-SH	brain:	n/a	chr2:179710249-179710265 chr2:179710247-179710268 chr2:179710254-179710261 chr2:179710711-179710721 chr2:179710254-179710261 chr2:179710254-179710261
4	REST	chr2:179710197-179711277	H1-neurons	neurons:	n/a	n/a
5	GATA3	chr2:179710119-179710760	SK-N-SH	brain:	n/a	chr2:179710249-179710265 chr2:179710247-179710268 chr2:179710254-179710261 chr2:179710711-179710721 chr2:179710254-179710261 chr2:179710254-179710261
6	REST	chr2:179710496-179710942	H1-neurons	neurons:	n/a	n/a
7	FOSL2	chr2:179710264-179710741	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr2:179710446-179710988	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CCDC141	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10165177	0.87[ASW][hapmap];0.87[CEU][hapmap];0.83[TSI][hapmap]
rs10497526	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10803920	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11884950	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693171	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489483	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1489486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1565287	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17362588	0.81[CEU][hapmap]
rs2291306	1.00[CHD][hapmap]
rs4637162	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4894054	0.87[ASW][hapmap]
rs4894055	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4894057	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4894060	0.83[EUR][1000 genomes]
rs56345539	0.89[EUR][1000 genomes]
rs6707222	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734390	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6747791	1.00[JPT][hapmap]
rs72957359	1.00[ASN][1000 genomes]
rs7570928	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7573700	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs966449	1.00[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6433738	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179693400-179712600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:179693400-179726000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:179694200-179713400	Weak transcription	Spleen	Spleen
4	chr2:179695600-179712600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:179695600-179712600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:179695600-179713000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:179695800-179711000	Weak transcription	Right Ventricle	heart
8	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:179696400-179728800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:179701800-179712000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:179701800-179712200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:179702200-179713200	Weak transcription	Fetal Thymus	thymus
13	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
14	chr2:179702400-179729200	Weak transcription	Lung	lung
15	chr2:179702400-179730000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:179702800-179728600	Weak transcription	Pancreas	Pancrea
17	chr2:179703400-179712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:179704400-179720800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:179707200-179721000	Strong transcription	Primary T cells from cord blood	blood
20	chr2:179707800-179711200	Enhancers	Brain Germinal Matrix	brain
21	chr2:179708000-179711600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:179708000-179727800	Weak transcription	Psoas Muscle	Psoas
23	chr2:179708200-179712000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:179708600-179711800	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:179708800-179711200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:179709000-179711200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:179709000-179711400	Enhancers	Colon Smooth Muscle	Colon
28	chr2:179709000-179711400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:179709000-179711400	Enhancers	Fetal Muscle Leg	muscle
30	chr2:179709000-179711600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:179709000-179712000	Enhancers	HSMMtube	muscle
32	chr2:179709200-179711000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:179709200-179711000	Enhancers	Fetal Brain Female	brain
34	chr2:179709200-179711200	Enhancers	Brain Hippocampus Middle	brain
35	chr2:179709200-179711400	Enhancers	Fetal Brain Male	brain
36	chr2:179709200-179711600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:179709200-179711600	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:179709200-179711600	Enhancers	HSMM	muscle
39	chr2:179709200-179711600	Enhancers	NHDF-Ad	bronchial
40	chr2:179709200-179711600	Enhancers	Osteobl	bone
41	chr2:179709400-179711000	Weak transcription	Left Ventricle	heart
42	chr2:179709400-179711200	Enhancers	NHLF	lung
43	chr2:179709400-179714800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:179709600-179710800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:179709600-179710800	Enhancers	Fetal Lung	lung
46	chr2:179709800-179711600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:179710000-179710800	Enhancers	Fetal Intestine Small	intestine
48	chr2:179710000-179710800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:179710000-179711200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:179710000-179711400	Enhancers	H9 Cell Line	embryonic stem cell

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