Variant report

Variant	rs17643558
Chromosome Location	chr3:43417792-43417793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43411353..43414757-chr3:43415544..43419725,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1026887	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1038202	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11706123	0.80[ASN][1000 genomes]
rs11706130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11708097	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11708173	0.90[GIH][hapmap];0.85[LWK][hapmap]
rs11709165	0.82[ASN][1000 genomes]
rs11709517	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11710079	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11710107	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11710486	0.85[ASN][1000 genomes]
rs11710955	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11711651	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11711758	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11712894	0.82[ASN][1000 genomes]
rs11713382	0.80[ASN][1000 genomes]
rs11714015	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs11717380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11717449	0.80[ASN][1000 genomes]
rs11718482	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11719258	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13061553	0.82[ASN][1000 genomes]
rs13079636	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13084604	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs13092838	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs13098202	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1384434	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1471643	0.80[ASN][1000 genomes]
rs1471644	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1482648	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1482650	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1482652	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1506616	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17407745	0.80[ASN][1000 genomes]
rs17407870	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs17407912	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2054554	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2086653	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2219902	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2372433	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2888312	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs34548104	0.80[ASN][1000 genomes]
rs34898315	0.80[ASN][1000 genomes]
rs35015014	0.80[ASN][1000 genomes]
rs35323779	0.89[ASN][1000 genomes]
rs35690908	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3772165	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3772167	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3821381	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4564953	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4682892	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs6441775	0.83[ASN][1000 genomes]
rs67032102	0.80[ASN][1000 genomes]
rs6767983	0.80[ASN][1000 genomes]
rs6768557	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs6775337	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6781290	0.82[ASN][1000 genomes]
rs6782442	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6797855	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6809134	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs73075063	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7428158	0.86[GIH][hapmap]
rs7616708	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7621271	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7653738	0.90[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs9311341	0.90[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17643558	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43391600-43436000	Weak transcription	Colonic Mucosa	Colon
2	chr3:43392200-43419600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:43400000-43419400	Weak transcription	Primary T cells from cord blood	blood
4	chr3:43403000-43419400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:43405000-43419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:43408200-43419200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:43408200-43419800	Weak transcription	NHLF	lung
8	chr3:43408400-43418200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:43408400-43419600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:43408600-43431200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:43408800-43429800	Weak transcription	Right Ventricle	heart
12	chr3:43408800-43431000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:43409200-43420400	Weak transcription	HSMMtube	muscle
14	chr3:43411600-43419600	Weak transcription	Left Ventricle	heart
15	chr3:43411800-43421000	Weak transcription	Lung	lung
16	chr3:43413000-43419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:43414200-43419200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:43414400-43418200	Weak transcription	Thymus	Thymus
19	chr3:43414400-43418800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:43414400-43419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:43415200-43418800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:43415200-43420400	Weak transcription	NH-A	brain
23	chr3:43415400-43419200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:43415400-43419600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:43415400-43420000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:43415400-43420200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:43415400-43420200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:43415400-43420200	Weak transcription	Fetal Stomach	stomach
29	chr3:43415400-43420200	Weak transcription	Right Atrium	heart
30	chr3:43415400-43421000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:43415600-43419400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:43415600-43419400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:43415600-43419400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:43415600-43419400	Weak transcription	Osteobl	bone
35	chr3:43415600-43419600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:43415600-43419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:43415600-43420000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:43415600-43420200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:43415600-43420200	Weak transcription	HSMM	muscle
40	chr3:43415800-43419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:43415800-43419800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:43415800-43419800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:43415800-43419800	Weak transcription	HUVEC	blood vessel
44	chr3:43415800-43420000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:43416200-43420800	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:43417000-43420200	Enhancers	Fetal Thymus	thymus
47	chr3:43417200-43419000	Weak transcription	Stomach Smooth Muscle	stomach

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