Variant report

Variant	rs4685400
Chromosome Location	chr3:16947451-16947452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:16938490..16940916-chr3:16946789..16948310,2	K562	blood:
2	chr3:16938490..16940162-chr3:16945952..16948289,2	K562	blood:
3	chr3:16946510..16948646-chr3:16954860..16957312,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10865746	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11926952	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12233492	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12487288	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs12497667	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13058764	0.83[JPT][hapmap]
rs13080108	0.90[JPT][hapmap]
rs1348109	0.93[ASN][1000 genomes]
rs1441035	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1441039	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17272796	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1806556	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1837698	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2014490	0.95[TSI][hapmap]
rs2881771	0.81[EUR][1000 genomes]
rs34149515	0.90[ASN][1000 genomes]
rs3924971	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4353792	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4461404	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs4472039	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4535211	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4602367	0.85[JPT][hapmap]
rs4618210	0.80[JPT][hapmap]
rs4685404	0.85[JPT][hapmap]
rs4685409	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4685427	0.80[JPT][hapmap]
rs6442660	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6762816	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6780191	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs6783752	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809087	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7610811	0.82[CHB][hapmap]
rs7611127	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs7612044	0.84[JPT][hapmap]
rs7617672	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7629676	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653027	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs9810017	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9830460	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs983545	0.81[EUR][1000 genomes]
rs9841259	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9854760	0.94[JPT][hapmap]
rs9862613	0.88[JPT][hapmap]
rs9879150	0.80[JPT][hapmap]
rs9880307	0.86[CHD][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs9882937	0.81[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4685400	SGOL1	cis	cerebellum	SCAN
rs4685400	TMEM43	cis	cerebellum	SCAN
rs4685400	CHCHD4	cis	parietal	SCAN
rs4685400	C3orf20	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16928000-16948800	Weak transcription	Lung	lung
2	chr3:16931200-16952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:16933800-16948200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:16936200-16949600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:16937400-16949400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:16939200-16948400	Weak transcription	Fetal Stomach	stomach
7	chr3:16939400-16950000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:16939800-16948800	Weak transcription	Fetal Kidney	kidney
9	chr3:16940400-16948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:16940800-16948400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:16940800-16950000	Weak transcription	Esophagus	oesophagus
12	chr3:16940800-16954200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:16940800-16962200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:16941200-16948200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:16941800-16959400	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:16942000-16947600	Enhancers	Ovary	ovary
17	chr3:16942200-16947600	Enhancers	Psoas Muscle	Psoas
18	chr3:16942800-16947800	Enhancers	Brain Germinal Matrix	brain
19	chr3:16942800-16952000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:16943000-16947600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:16943000-16948400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:16943000-16948800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:16943200-16952200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:16943400-16948200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:16943400-16948600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:16943400-16950400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:16943600-16948000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:16943600-16948200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:16943600-16948200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:16943600-16948200	Weak transcription	Small Intestine	intestine
31	chr3:16943600-16948200	Weak transcription	Dnd41	blood
32	chr3:16943600-16948400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:16943600-16948800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:16943600-16948800	Weak transcription	Gastric	stomach
35	chr3:16943600-16948800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:16943600-16950000	Weak transcription	Placenta	Placenta
37	chr3:16943600-16952600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr3:16943800-16947600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:16943800-16948400	Enhancers	Primary T cells from cord blood	blood
40	chr3:16943800-16948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:16943800-16948600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:16943800-16950200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:16943800-16954200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:16944200-16948200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:16944400-16947600	Enhancers	Left Ventricle	heart
46	chr3:16944400-16948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:16944400-16949000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr3:16944600-16948200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:16945000-16947800	Enhancers	Right Atrium	heart
50	chr3:16945400-16949000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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