Variant report

Variant	rs661929
Chromosome Location	chr2:20970053-20970054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20964364..20967135-chr2:20968385..20970753,2	K562	blood:
2	chr2:20963398..20967135-chr2:20967527..20970753,3	K562	blood:
3	chr2:20969082..20971469-chr2:20973504..20975005,2	K562	blood:
4	chr2:20968724..20971048-chr2:21033483..21035805,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1098155	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468977	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472693	1.00[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16988063	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16988078	0.81[EUR][1000 genomes]
rs514459	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs535022	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61662529	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs661929	MFSD2B	cis	parietal	SCAN
rs661929	C2orf43	cis	parietal	SCAN
rs661929	FLJ21820	cis	multi-tissue	Pritchard
rs661929	GEN1	cis	parietal	SCAN
rs661929	C2orf43	cis	Frontal Cortex	GTEx
rs661929	RHOB	cis	parietal	SCAN
rs661929	C2orf43	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20899800-20972400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:20902400-20971800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:20917600-20971800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20926200-20977000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:20926400-20995000	Weak transcription	Hela-S3	cervix
6	chr2:20937200-20974400	Weak transcription	HSMM	muscle
7	chr2:20946600-20972200	Weak transcription	Esophagus	oesophagus
8	chr2:20949200-20979200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:20950600-20971600	Weak transcription	Fetal Kidney	kidney
10	chr2:20951000-20972400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:20951600-20973600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:20951800-20993200	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:20952400-20970600	Weak transcription	Fetal Lung	lung
14	chr2:20952800-20972200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:20952800-20972400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:20952800-20974000	Weak transcription	A549	lung
17	chr2:20952800-20990400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:20953000-20972200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:20953000-20989400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:20954200-21001200	Weak transcription	NH-A	brain
21	chr2:20957800-20973600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:20957800-20988400	Weak transcription	Left Ventricle	heart
23	chr2:20957800-20988800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:20958400-20977600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:20958600-20995800	Weak transcription	HMEC	breast
26	chr2:20959000-20995400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:20959200-20973600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:20959200-20997000	Weak transcription	Brain Substantia Nigra	brain
29	chr2:20959800-20972800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:20960400-20977200	Weak transcription	Stomach Mucosa	stomach
31	chr2:20960600-20972200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:20960600-20972200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:20960600-20983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:20960600-20989200	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:20960800-20970400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:20960800-20971800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:20960800-20972200	Weak transcription	Liver	Liver
38	chr2:20960800-20973000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:20960800-20978200	Weak transcription	NHEK	skin
40	chr2:20960800-20989000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:20960800-20996200	Weak transcription	HSMMtube	muscle
42	chr2:20961000-20972000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:20961200-20973600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:20961400-20971600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:20961400-20972200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:20961400-20972800	Weak transcription	K562	blood
47	chr2:20963400-20974000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:20963400-20976600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:20964000-20981600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:20964000-20996000	Weak transcription	Osteobl	bone

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