Variant report

Variant	rs6554107
Chromosome Location	chr4:54296120-54296121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10008334	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10012853	0.82[EUR][1000 genomes]
rs10517296	0.81[EUR][1000 genomes]
rs11133267	0.81[EUR][1000 genomes]
rs11737139	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11935822	0.82[EUR][1000 genomes]
rs11942086	0.81[EUR][1000 genomes]
rs11944047	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11946199	0.82[EUR][1000 genomes]
rs12507723	0.82[EUR][1000 genomes]
rs13117240	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13119372	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13120051	0.82[EUR][1000 genomes]
rs13130836	0.82[EUR][1000 genomes]
rs1399241	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2128103	0.82[EUR][1000 genomes]
rs2271555	0.82[EUR][1000 genomes]
rs2412489	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28404076	0.82[ASN][1000 genomes]
rs34173240	0.83[EUR][1000 genomes]
rs34317954	0.82[EUR][1000 genomes]
rs35033239	0.82[EUR][1000 genomes]
rs35225781	0.82[EUR][1000 genomes]
rs3986364	0.81[EUR][1000 genomes]
rs6420001	0.82[EUR][1000 genomes]
rs6554095	0.82[EUR][1000 genomes]
rs6554096	0.82[EUR][1000 genomes]
rs6554103	0.82[EUR][1000 genomes]
rs6554109	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810557	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834099	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835629	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6846569	0.82[EUR][1000 genomes]
rs6847289	0.82[EUR][1000 genomes]
rs7684894	0.82[EUR][1000 genomes]
rs7694840	0.82[EUR][1000 genomes]
rs997832	0.82[EUR][1000 genomes]
rs9992820	0.82[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554107	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	chr4:54244600-54310600	Weak transcription	Spleen	Spleen
2	chr4:54244600-54319200	Weak transcription	Pancreas	Pancrea
3	chr4:54246200-54319200	Weak transcription	Aorta	Aorta
4	chr4:54246600-54311200	Weak transcription	Small Intestine	intestine
5	chr4:54253400-54327200	Weak transcription	Colonic Mucosa	Colon
6	chr4:54256600-54306200	Weak transcription	Stomach Mucosa	stomach
7	chr4:54256600-54319200	Weak transcription	Gastric	stomach
8	chr4:54267800-54302400	Weak transcription	Psoas Muscle	Psoas
9	chr4:54268000-54310400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:54268000-54327600	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:54268400-54319800	Weak transcription	A549	lung
12	chr4:54269400-54303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:54270000-54330800	Weak transcription	Brain Substantia Nigra	brain
14	chr4:54270200-54316600	Weak transcription	Esophagus	oesophagus
15	chr4:54276400-54319000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:54276600-54297000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:54276600-54302200	Weak transcription	Fetal Brain Female	brain
18	chr4:54276600-54319000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:54276600-54319000	Weak transcription	Lung	lung
20	chr4:54276800-54310600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:54276800-54316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:54276800-54324800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:54277800-54296600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:54283000-54296200	Weak transcription	Brain Germinal Matrix	brain
25	chr4:54286200-54303000	Weak transcription	Fetal Stomach	stomach
26	chr4:54286200-54310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:54286200-54316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:54287800-54310400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:54288200-54307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:54288200-54310800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:54290400-54296600	Strong transcription	Dnd41	blood
32	chr4:54291000-54300000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:54291000-54310600	Weak transcription	Right Ventricle	heart
34	chr4:54291400-54302800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:54291400-54313200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:54291600-54297000	Strong transcription	GM12878-XiMat	blood
37	chr4:54291600-54298400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:54291800-54297600	Strong transcription	Osteobl	bone
39	chr4:54291800-54302000	Strong transcription	NHDF-Ad	bronchial
40	chr4:54291800-54315000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:54291800-54329400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:54292000-54296600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:54292000-54297000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:54292000-54299000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:54292000-54299600	Strong transcription	Primary B cells from cord blood	blood
46	chr4:54292000-54300200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:54292000-54302200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:54292000-54314400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:54292200-54296800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:54292200-54297000	Strong transcription	Liver	Liver

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