Variant report

Variant	rs3125635
Chromosome Location	chr1:47789644-47789645
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47789007..47791037-chr1:47792198..47794063,2	MCF-7	breast:
2	chr1:47695594..47698259-chr1:47788748..47790868,3	K562	blood:
3	chr1:47777717..47780108-chr1:47788824..47790541,2	K562	blood:
4	chr1:47748082..47750249-chr1:47787752..47790468,2	K562	blood:
5	chr1:47788958..47792028-chr1:47798219..47801724,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123473	Chromatin interaction
ENSG00000162367	Chromatin interaction
ENSG00000162368	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10157883	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1028646	0.85[ASN][1000 genomes]
rs1028647	0.85[ASN][1000 genomes]
rs10399673	0.81[JPT][hapmap]
rs10789507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10890475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890476	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890477	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890478	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211508	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211517	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11211520	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211521	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211522	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211523	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211524	0.95[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578038	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582877	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024163	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12039726	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12040451	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042624	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046294	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12047319	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048407	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12409549	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12566521	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306470	0.88[ASN][1000 genomes]
rs2406105	0.86[ASN][1000 genomes]
rs2472725	0.95[JPT][hapmap]
rs2472730	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472731	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2494246	0.80[ASN][1000 genomes]
rs2494247	0.85[ASN][1000 genomes]
rs2622925	0.95[JPT][hapmap]
rs2742099	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742103	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742104	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2758735	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2758736	0.83[ASN][1000 genomes]
rs2758737	0.85[ASN][1000 genomes]
rs2758744	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798349	0.82[MEX][hapmap]
rs2820989	0.95[JPT][hapmap]
rs2821087	0.85[ASN][1000 genomes]
rs2821088	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2821089	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2821090	0.85[ASN][1000 genomes]
rs2821092	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2821093	0.95[JPT][hapmap]
rs2897237	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3088062	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.87[ASN][1000 genomes]
rs3122607	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3122611	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3122615	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3122616	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3122619	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3122620	0.89[ASN][1000 genomes]
rs3122623	0.84[ASN][1000 genomes]
rs3125624	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3125628	0.90[JPT][hapmap]
rs3125630	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3125631	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3125632	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3125633	0.95[JPT][hapmap]
rs3125636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3125638	0.81[ASN][1000 genomes]
rs3125641	0.86[ASN][1000 genomes]
rs3125644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35880845	0.88[ASN][1000 genomes]
rs3923691	0.88[AMR][1000 genomes]
rs3925058	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4463720	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4492666	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4600090	0.86[MEX][hapmap]
rs4603175	0.81[JPT][hapmap]
rs4926836	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926839	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56987466	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58688029	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59492977	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61284456	0.89[EUR][1000 genomes]
rs61782712	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61782733	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61784774	0.86[EUR][1000 genomes]
rs6588348	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6660321	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6671254	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6673882	0.81[JPT][hapmap]
rs6690084	0.86[MEX][hapmap]
rs6697248	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7511699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525650	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7532148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541522	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541748	0.89[ASN][1000 genomes]
rs7545281	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436394	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436430	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9436749	0.86[ASN][1000 genomes]
rs9436882	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3125635	CMPK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47780600-47798000	Weak transcription	HSMMtube	muscle
3	chr1:47780800-47791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:47780800-47797800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:47787200-47790800	Enhancers	Stomach Mucosa	stomach
6	chr1:47788200-47791800	Enhancers	Fetal Intestine Small	intestine
7	chr1:47788600-47792400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr1:47788800-47789800	Enhancers	K562	blood
9	chr1:47788800-47790200	Enhancers	Fetal Intestine Large	intestine
10	chr1:47789200-47789800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:47789200-47790600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr1:47789200-47792400	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:47789600-47791400	Weak transcription	A549	lung

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