Variant report

Variant	rs997832
Chromosome Location	chr4:54248276-54248277
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10012853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013573	0.84[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10028214	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1014056	0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10517296	0.84[CHB][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133267	0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935822	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946199	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12499401	0.84[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12501431	0.81[EUR][1000 genomes]
rs12507723	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13120051	0.84[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125807	0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13130836	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351514	0.84[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1514387	0.81[YRI][hapmap]
rs1514388	0.81[YRI][hapmap]
rs1514389	0.81[YRI][hapmap]
rs17082659	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082910	0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2128103	0.84[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170421	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271555	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271557	0.84[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2292579	0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34028346	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34173240	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34317954	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033239	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35089532	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35225781	0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313782	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3817270	0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3946758	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]
rs3986364	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6420001	0.84[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554095	0.84[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554096	0.84[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554102	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554103	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554107	0.82[EUR][1000 genomes]
rs6554108	0.84[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846569	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71597836	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678953	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679743	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684450	0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684894	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694840	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967018	0.86[YRI][hapmap]
rs980988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992820	0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997358	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9997844	0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs997832	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54244600-54250200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:54244600-54250200	Weak transcription	Left Ventricle	heart
3	chr4:54244600-54256000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54244600-54256000	Weak transcription	Esophagus	oesophagus
5	chr4:54244600-54256000	Weak transcription	Gastric	stomach
6	chr4:54244600-54256000	Weak transcription	Lung	lung
7	chr4:54244600-54256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:54244600-54272800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:54244600-54310600	Weak transcription	Spleen	Spleen
10	chr4:54244600-54319200	Weak transcription	Pancreas	Pancrea
11	chr4:54244800-54250200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:54244800-54256000	Weak transcription	Stomach Mucosa	stomach
13	chr4:54245000-54248400	Weak transcription	Placenta	Placenta
14	chr4:54245000-54248400	Weak transcription	HSMM	muscle
15	chr4:54245000-54248800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:54245000-54249800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:54245000-54252800	Weak transcription	Brain Angular Gyrus	brain
18	chr4:54245000-54271400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:54245200-54248400	Weak transcription	Adipose Nuclei	Adipose
20	chr4:54245200-54248400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:54245200-54249400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:54245200-54250200	Weak transcription	Fetal Stomach	stomach
23	chr4:54245200-54252800	Weak transcription	HSMMtube	muscle
24	chr4:54245400-54248400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:54245400-54248400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:54245400-54248400	Weak transcription	Fetal Thymus	thymus
27	chr4:54245400-54248600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:54245400-54249600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:54245400-54251800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:54245400-54253000	Weak transcription	Colonic Mucosa	Colon
31	chr4:54245400-54253000	Weak transcription	Psoas Muscle	Psoas
32	chr4:54245400-54256000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:54245400-54279400	Weak transcription	Right Ventricle	heart
34	chr4:54245600-54248600	Weak transcription	A549	lung
35	chr4:54245600-54252800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:54245600-54269600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:54245600-54270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:54245800-54248400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:54245800-54248400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:54245800-54248400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:54245800-54249400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:54246000-54248400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:54246000-54248600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:54246000-54250000	Weak transcription	Fetal Kidney	kidney
45	chr4:54246000-54257800	Weak transcription	Fetal Heart	heart
46	chr4:54246000-54270200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:54246000-54270200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:54246200-54250600	Weak transcription	Brain Substantia Nigra	brain
49	chr4:54246200-54251600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:54246200-54252800	Weak transcription	Fetal Brain Female	brain

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