Variant report

Variant	rs9997358
Chromosome Location	chr4:54310633-54310634
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54309949..54312733-chr4:54313192..54317009,3	K562	blood:
2	chr4:54230700..54232277-chr4:54310392..54312931,2	K562	blood:
3	chr4:54229357..54232277-chr4:54310392..54313352,3	K562	blood:

Variant related genes	Relation type
ENSG00000184178	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10012853	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10013573	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10028214	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1014056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10517296	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133267	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11935822	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11942086	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11946199	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12499401	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12501431	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12507723	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13120051	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13125807	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13130836	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1351514	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17082659	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17082910	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2128103	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2170421	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271555	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271557	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292579	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34028346	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34173240	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34317954	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35033239	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35089532	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35225781	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35313782	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36090882	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3946758	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3986364	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6420001	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554095	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554096	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554102	0.85[ASN][1000 genomes]
rs6554103	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554108	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846569	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6847289	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71597836	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7678953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679743	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7684450	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684894	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7694840	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs980988	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs997832	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9992820	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997844	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9997358	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54244600-54319200	Weak transcription	Pancreas	Pancrea
2	chr4:54246200-54319200	Weak transcription	Aorta	Aorta
3	chr4:54246600-54311200	Weak transcription	Small Intestine	intestine
4	chr4:54253400-54327200	Weak transcription	Colonic Mucosa	Colon
5	chr4:54256600-54319200	Weak transcription	Gastric	stomach
6	chr4:54268000-54327600	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:54268400-54319800	Weak transcription	A549	lung
8	chr4:54270000-54330800	Weak transcription	Brain Substantia Nigra	brain
9	chr4:54270200-54316600	Weak transcription	Esophagus	oesophagus
10	chr4:54276400-54319000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:54276600-54319000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:54276600-54319000	Weak transcription	Lung	lung
13	chr4:54276800-54316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:54276800-54324800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:54286200-54310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:54286200-54316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:54288200-54310800	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:54291400-54313200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:54291800-54315000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:54291800-54329400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:54292000-54314400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:54292200-54331200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:54294000-54325600	Weak transcription	Fetal Heart	heart
24	chr4:54294400-54320600	Weak transcription	HSMMtube	muscle
25	chr4:54295200-54331600	Weak transcription	Hela-S3	cervix
26	chr4:54295400-54316600	Weak transcription	Ovary	ovary
27	chr4:54295600-54311400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:54295600-54316600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:54295600-54319800	Weak transcription	Brain Anterior Caudate	brain
30	chr4:54295600-54339400	Weak transcription	Fetal Brain Male	brain
31	chr4:54296800-54320400	Weak transcription	Brain Germinal Matrix	brain
32	chr4:54297400-54312600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:54297400-54312800	Strong transcription	Primary T cells from cord blood	blood
34	chr4:54297400-54319200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:54297400-54319200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:54297400-54319200	Weak transcription	NH-A	brain
37	chr4:54297600-54310800	Weak transcription	HUVEC	blood vessel
38	chr4:54297600-54326200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:54297600-54329600	Strong transcription	Dnd41	blood
40	chr4:54298000-54310800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:54298200-54311200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:54298600-54329600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:54301000-54311600	Weak transcription	Fetal Intestine Small	intestine
44	chr4:54301800-54313800	Strong transcription	Liver	Liver
45	chr4:54302800-54320600	Weak transcription	Psoas Muscle	Psoas
46	chr4:54303000-54311200	Weak transcription	Fetal Brain Female	brain
47	chr4:54303400-54310800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:54303600-54311000	Strong transcription	NHDF-Ad	bronchial
49	chr4:54304000-54314000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:54304000-54315000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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