Variant report

Variant	rs3946758
Chromosome Location	chr4:54343907-54343908
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54319802..54322613-chr4:54343066..54345162,2	K562	blood:
2	chr4:54340192..54342016-chr4:54343724..54345508,2	K562	blood:
3	chr4:54341936..54344019-chr4:54348085..54349647,2	MCF-7	breast:
4	chr4:54340153..54341692-chr4:54343827..54345508,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10012853	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10013573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10028214	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10517291	0.85[CHB][hapmap]
rs10517292	0.85[CHB][hapmap]
rs10517296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11133267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737139	0.80[EUR][1000 genomes]
rs11935822	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11942086	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11946199	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12499401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501431	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507723	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13120051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13125807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130836	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1351514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1514387	0.96[YRI][hapmap]
rs1514388	0.96[YRI][hapmap]
rs1514389	0.96[YRI][hapmap]
rs17082565	0.84[CHB][hapmap]
rs17082659	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17082910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2128103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2170421	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2271555	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412489	0.81[EUR][1000 genomes]
rs34028346	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34173240	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34317954	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35033239	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35089532	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35225781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35313782	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36090882	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3817270	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3986364	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4864747	0.84[CHB][hapmap]
rs6420001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554095	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6554096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554099	0.81[YRI][hapmap]
rs6554103	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554109	0.81[EUR][1000 genomes]
rs6810557	0.81[EUR][1000 genomes]
rs6846569	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6847289	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6852884	0.84[YRI][hapmap]
rs71597836	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7678953	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679743	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7684450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7684894	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7694840	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs967018	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs980988	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs997832	0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9992820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9997358	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3946758	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54320000-54353200	Weak transcription	Gastric	stomach
2	chr4:54327600-54347800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
6	chr4:54329600-54351000	Weak transcription	Adipose Nuclei	Adipose
7	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
9	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
10	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:54338400-54347400	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:54341400-54347800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:54341800-54345800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:54341800-54348000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:54342000-54348200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:54342400-54347000	Enhancers	HSMM	muscle
17	chr4:54342600-54345200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:54342600-54347800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:54342800-54344000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:54343000-54344000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:54343000-54345800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:54343000-54346800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
25	chr4:54343200-54344400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:54343200-54344800	Weak transcription	Fetal Intestine Small	intestine
27	chr4:54343200-54345200	Weak transcription	K562	blood
28	chr4:54343200-54345400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:54343200-54345400	Weak transcription	A549	lung
30	chr4:54343200-54345800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:54343200-54347800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:54343200-54348000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
34	chr4:54343400-54344600	Weak transcription	Liver	Liver
35	chr4:54343400-54345400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:54343400-54345600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr4:54343400-54346600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:54343400-54347000	Weak transcription	Pancreas	Pancrea
39	chr4:54343400-54347600	Enhancers	NH-A	brain
40	chr4:54343400-54347800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:54343400-54347800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr4:54343400-54347800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:54343400-54347800	Enhancers	Osteobl	bone
44	chr4:54343400-54352200	Weak transcription	Esophagus	oesophagus
45	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:54343600-54344000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:54343600-54344000	Enhancers	NHLF	lung
48	chr4:54343600-54344200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:54343600-54344400	Weak transcription	Fetal Intestine Large	intestine
50	chr4:54343600-54345400	Enhancers	HUES6 Cell Line	embryonic stem cell

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