Variant report

Variant	rs6734390
Chromosome Location	chr2:179711748-179711749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10165177	0.87[ASW][hapmap];0.87[CEU][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10497526	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10803920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884950	0.88[EUR][1000 genomes]
rs12469367	1.00[CHB][hapmap]
rs12693171	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][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[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17362588	0.81[CEU][hapmap]
rs2291306	1.00[CHD][hapmap]
rs4637162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894054	0.87[ASW][hapmap];0.80[MKK][hapmap]
rs4894055	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894057	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894060	0.87[EUR][1000 genomes]
rs56345539	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433738	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]
rs6707222	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6747791	1.00[JPT][hapmap]
rs7570928	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
3	nsv521818	chr2:179710973-179713601	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6734390	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

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	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
8	chr2:179696400-179728800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:179701800-179712000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:179701800-179712200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:179702200-179713200	Weak transcription	Fetal Thymus	thymus
12	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
13	chr2:179702400-179729200	Weak transcription	Lung	lung
14	chr2:179702400-179730000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:179702800-179728600	Weak transcription	Pancreas	Pancrea
16	chr2:179703400-179712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:179704400-179720800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179707200-179721000	Strong transcription	Primary T cells from cord blood	blood
19	chr2:179708000-179727800	Weak transcription	Psoas Muscle	Psoas
20	chr2:179708200-179712000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:179708600-179711800	Enhancers	Stomach Smooth Muscle	stomach
22	chr2:179709000-179712000	Enhancers	HSMMtube	muscle
23	chr2:179709400-179714800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:179710000-179714200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:179710200-179715000	Weak transcription	Ovary	ovary
26	chr2:179710400-179712000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:179710600-179711800	Weak transcription	Aorta	Aorta
28	chr2:179710800-179712600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:179710800-179722400	Weak transcription	Fetal Lung	lung
30	chr2:179710800-179724000	Weak transcription	Fetal Intestine Small	intestine
31	chr2:179710800-179782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:179711000-179712200	Enhancers	Left Ventricle	heart
33	chr2:179711200-179712000	Enhancers	Fetal Heart	heart
34	chr2:179711200-179714400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:179711200-179715000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:179711400-179711800	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:179711400-179712800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:179711400-179714800	Weak transcription	Fetal Brain Male	brain
39	chr2:179711400-179719400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:179711400-179720600	Weak transcription	Right Ventricle	heart
41	chr2:179711600-179712000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:179711600-179713800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:179711600-179719800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:179711600-179723800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:179711600-179728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:179711600-179728400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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