Variant report

Variant	rs2742104
Chromosome Location	chr1:47735280-47735281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47734637..47736939-chr1:47798591..47800352,2	K562	blood:
2	chr1:47656858..47659851-chr1:47734619..47737417,2	K562	blood:
3	chr1:47734504..47737018-chr1:47737224..47739199,2	K562	blood:

Variant related genes	Relation type
ENSG00000162368	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10157883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028646	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1028647	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10399673	0.81[JPT][hapmap]
rs1044457	0.93[TSI][hapmap]
rs10789507	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10890475	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10890476	0.89[ASN][1000 genomes]
rs10890478	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11211504	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11211508	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11211510	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211511	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211513	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11211517	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211520	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11211524	0.86[CHB][hapmap]
rs11578038	0.85[ASN][1000 genomes]
rs11582877	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12024163	0.84[ASN][1000 genomes]
rs12039726	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12040451	0.87[ASN][1000 genomes]
rs12042624	0.89[ASN][1000 genomes]
rs12047319	0.89[ASN][1000 genomes]
rs12118514	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12121831	0.80[EUR][1000 genomes]
rs12125261	0.96[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12126139	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12138072	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12141060	0.96[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12409549	0.86[ASN][1000 genomes]
rs12730819	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12732050	0.96[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12732410	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12743877	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17452995	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2246707	0.82[EUR][1000 genomes]
rs2472725	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472730	0.88[ASN][1000 genomes]
rs2472731	0.86[ASN][1000 genomes]
rs2494247	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622901	0.81[EUR][1000 genomes]
rs2622905	0.82[EUR][1000 genomes]
rs2622907	0.82[EUR][1000 genomes]
rs2622908	0.82[EUR][1000 genomes]
rs2622925	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2742081	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742099	0.88[ASN][1000 genomes]
rs2742103	0.91[ASN][1000 genomes]
rs2758735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2758736	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2758737	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2758744	0.91[ASN][1000 genomes]
rs2820987	0.82[EUR][1000 genomes]
rs2820988	0.82[EUR][1000 genomes]
rs2820989	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2821087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821089	0.89[ASN][1000 genomes]
rs2821090	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821093	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2821094	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2821096	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2897237	0.88[ASN][1000 genomes]
rs3088062	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3122607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3122610	0.82[EUR][1000 genomes]
rs3122611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3122615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3122616	0.89[ASN][1000 genomes]
rs3122619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122620	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3122623	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3125624	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125628	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3125630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3125631	0.89[ASN][1000 genomes]
rs3125632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3125633	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125635	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3125636	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3125638	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3125639	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3125640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3125641	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3125644	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34400183	0.82[EUR][1000 genomes]
rs34952704	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35711761	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35774681	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35880845	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3925058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147192	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4463720	0.83[ASN][1000 genomes]
rs4492666	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4603175	0.81[JPT][hapmap]
rs4926824	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926836	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs56987466	0.89[ASN][1000 genomes]
rs58688029	0.91[ASN][1000 genomes]
rs59492977	0.91[ASN][1000 genomes]
rs61782706	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61782712	0.91[ASN][1000 genomes]
rs61782733	0.82[ASN][1000 genomes]
rs6588348	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6588365	0.81[EUR][1000 genomes]
rs6659946	0.83[EUR][1000 genomes]
rs6660321	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6671254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673882	0.81[JPT][hapmap]
rs6681868	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6689687	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6692691	0.86[GIH][hapmap]
rs6692734	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6697248	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6703956	0.96[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6795	0.85[CEU][hapmap]
rs7511699	0.89[ASN][1000 genomes]
rs7525650	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7532148	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7541748	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7543016	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7545281	0.83[ASN][1000 genomes]
rs9436394	0.89[ASN][1000 genomes]
rs9436429	0.89[ASN][1000 genomes]
rs9436430	0.95[JPT][hapmap]
rs9436749	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436838	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9436882	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2742104	CMPK	Cis_1M	lymphoblastoid	RTeQTL
rs2742104	TMEM125	cis	cerebellum	SCAN
rs2742104	CMPK1	cis	lymphoblastoid	seeQTL
rs2742104	KNCN	cis	cerebellum	SCAN
rs2742104	CMPK1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47705200-47766400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47705600-47766400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:47709800-47745000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47712600-47742600	Weak transcription	Fetal Lung	lung
5	chr1:47712800-47745600	Weak transcription	Fetal Brain Female	brain
6	chr1:47713000-47736400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:47713200-47745800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:47713800-47745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:47714400-47779200	Weak transcription	Small Intestine	intestine
10	chr1:47714600-47745800	Weak transcription	Primary B cells from cord blood	blood
11	chr1:47714600-47778400	Weak transcription	Fetal Heart	heart
12	chr1:47714800-47741200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:47714800-47742800	Weak transcription	Fetal Kidney	kidney
14	chr1:47714800-47746000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:47715400-47740000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:47715600-47749200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:47715800-47735400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:47716600-47739200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:47716600-47772600	Strong transcription	Dnd41	blood
20	chr1:47716800-47739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:47717000-47745800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:47718200-47746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:47718800-47739800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:47719800-47745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:47720400-47741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:47720400-47757000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:47720600-47766400	Weak transcription	Brain Germinal Matrix	brain
28	chr1:47721000-47735400	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:47721000-47749000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:47721600-47766800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:47723400-47772400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:47724600-47739400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:47726000-47745200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:47726200-47745800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:47726600-47735400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:47726800-47745200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:47727000-47745800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:47728200-47742600	Weak transcription	GM12878-XiMat	blood
39	chr1:47728400-47745600	Weak transcription	NHLF	lung
40	chr1:47728600-47755200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:47729000-47738600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:47729000-47767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:47729200-47746000	Weak transcription	Placenta	Placenta
44	chr1:47730000-47736600	Weak transcription	NHEK	skin
45	chr1:47730400-47770200	Weak transcription	Colonic Mucosa	Colon
46	chr1:47730800-47755000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:47730800-47766400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:47731000-47738200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:47731400-47736600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:47731400-47738200	Strong transcription	Thymus	Thymus

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