Variant report

Variant	rs11944047
Chromosome Location	chr4:54349651-54349652
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10008334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10014172	0.85[YRI][hapmap]
rs10022604	0.96[YRI][hapmap]
rs10023613	0.85[YRI][hapmap]
rs10024153	0.82[LWK][hapmap];0.96[YRI][hapmap]
rs10025091	0.83[LWK][hapmap];0.96[YRI][hapmap]
rs10027090	0.85[YRI][hapmap]
rs10028131	0.81[YRI][hapmap]
rs10517295	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs11133274	0.80[JPT][hapmap]
rs11725230	0.81[GIH][hapmap]
rs11734039	0.81[GIH][hapmap]
rs11737139	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501431	0.81[EUR][1000 genomes]
rs12507739	0.81[GIH][hapmap]
rs12642437	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645252	0.81[YRI][hapmap]
rs12645287	0.82[YRI][hapmap]
rs12645694	0.82[YRI][hapmap]
rs12649335	0.85[YRI][hapmap]
rs13117240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119372	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125807	0.82[EUR][1000 genomes]
rs1399241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473911	0.82[YRI][hapmap]
rs15834	0.81[YRI][hapmap]
rs17082681	0.82[YRI][hapmap]
rs17082726	0.82[YRI][hapmap]
rs17082811	0.82[YRI][hapmap]
rs17082847	0.85[YRI][hapmap]
rs17082910	0.82[EUR][1000 genomes]
rs17839071	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs2048709	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs2054589	0.82[YRI][hapmap]
rs2271557	0.82[EUR][1000 genomes]
rs2292579	0.82[EUR][1000 genomes]
rs2412487	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs2412489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28404076	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28575132	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs28658460	0.82[YRI][hapmap]
rs34028346	0.82[EUR][1000 genomes]
rs35089532	0.82[EUR][1000 genomes]
rs35313782	0.82[EUR][1000 genomes]
rs3811785	0.81[GIH][hapmap]
rs4864760	0.81[GIH][hapmap]
rs4864766	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59585683	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554105	0.81[GIH][hapmap]
rs6554107	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554109	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6810557	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816889	0.81[YRI][hapmap]
rs6828559	0.81[GIH][hapmap]
rs6834099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835629	0.87[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682199	0.81[GIH][hapmap]
rs931181	0.81[GIH][hapmap]
rs9312639	0.81[GIH][hapmap]
rs9312640	0.82[YRI][hapmap]
rs9996049	0.81[YRI][hapmap]
rs9997905	0.82[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11944047	SCFD2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54320000-54353200	Weak transcription	Gastric	stomach
2	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:54329600-54351000	Weak transcription	Adipose Nuclei	Adipose
6	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
8	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
9	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
12	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
13	chr4:54343400-54352200	Weak transcription	Esophagus	oesophagus
14	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:54343600-54352600	Weak transcription	Placenta	Placenta
16	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:54345600-54352200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:54345800-54349800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:54345800-54351000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:54345800-54355400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:54346000-54356400	Weak transcription	HSMMtube	muscle
22	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
23	chr4:54346600-54350600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:54347000-54349800	Weak transcription	NHEK	skin
25	chr4:54347200-54351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:54347800-54349800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:54347800-54349800	Weak transcription	Osteobl	bone
29	chr4:54347800-54351000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:54347800-54355000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:54348000-54349800	Weak transcription	HMEC	breast
32	chr4:54348000-54353400	Weak transcription	Pancreas	Pancrea
33	chr4:54348000-54355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
35	chr4:54348200-54349800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:54348200-54359600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:54349000-54360000	Weak transcription	Liver	Liver
38	chr4:54349600-54352200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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