Variant report

Variant	rs6425625
Chromosome Location	chr1:180332045-180332046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180326464..180328252-chr1:180330976..180332567,2	K562	blood:
2	chr1:180326027..180329437-chr1:180330774..180333655,3	K562	blood:

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10158367	0.81[ASN][1000 genomes]
rs10494527	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs10737342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753209	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs10753211	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs10753212	0.82[ASN][1000 genomes]
rs10798745	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs10798746	0.90[CHB][hapmap]
rs10798752	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798753	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798754	1.00[ASN][1000 genomes]
rs10798756	0.83[ASN][1000 genomes]
rs10798757	0.83[ASN][1000 genomes]
rs10798759	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs10798760	0.82[ASN][1000 genomes]
rs10798761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798762	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10798766	0.82[ASN][1000 genomes]
rs10798767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798769	0.82[CHB][hapmap]
rs10913969	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10913970	0.89[ASN][1000 genomes]
rs10913974	0.83[ASN][1000 genomes]
rs10913976	0.83[ASN][1000 genomes]
rs10913978	0.83[ASN][1000 genomes]
rs10913980	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs10913981	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913982	0.83[ASN][1000 genomes]
rs10913983	0.83[ASN][1000 genomes]
rs10913984	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs10913985	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10913986	0.83[ASN][1000 genomes]
rs10913987	0.83[ASN][1000 genomes]
rs10913994	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10913998	0.81[ASN][1000 genomes]
rs10914001	0.82[ASN][1000 genomes]
rs10914002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10914005	0.82[CHB][hapmap]
rs10914007	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10914014	0.80[ASN][1000 genomes]
rs10914017	0.89[CHB][hapmap]
rs10914018	0.86[CHB][hapmap]
rs10914023	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs11580793	0.90[CHB][hapmap]
rs12024156	0.83[ASN][1000 genomes]
rs12034217	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs12034669	0.91[ASN][1000 genomes]
rs12039331	0.81[JPT][hapmap]
rs12039933	0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12045123	0.91[ASN][1000 genomes]
rs12045636	0.95[ASN][1000 genomes]
rs12085808	0.91[ASN][1000 genomes]
rs12091722	0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs12122338	0.82[ASN][1000 genomes]
rs12127886	0.82[ASN][1000 genomes]
rs12128560	0.82[ASN][1000 genomes]
rs12129511	0.82[ASN][1000 genomes]
rs12129784	0.83[ASN][1000 genomes]
rs12131071	0.82[ASN][1000 genomes]
rs12132837	0.80[ASN][1000 genomes]
rs12135463	0.82[ASN][1000 genomes]
rs12142124	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402815	0.93[ASN][1000 genomes]
rs12403665	0.93[ASN][1000 genomes]
rs12404209	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12405902	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs12407122	0.91[ASN][1000 genomes]
rs12565492	0.86[CHB][hapmap]
rs12691484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730889	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs1341924	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1418102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538620	0.90[CHB][hapmap]
rs1890731	0.82[ASN][1000 genomes]
rs1925339	0.90[CHB][hapmap]
rs2296378	0.90[CHB][hapmap]
rs2794962	0.85[CHB][hapmap]
rs2794978	0.92[EUR][1000 genomes]
rs28506072	0.89[ASN][1000 genomes]
rs2877399	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877415	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3737584	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs3806300	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3923222	0.82[ASN][1000 genomes]
rs4058058	0.90[CHB][hapmap]
rs4076403	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs4142992	0.82[ASN][1000 genomes]
rs4418555	0.80[ASN][1000 genomes]
rs4420052	0.83[ASN][1000 genomes]
rs4421553	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs4424469	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4436345	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442335	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs4483365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543756	0.90[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4562579	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4578179	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs4593778	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4607831	0.82[ASN][1000 genomes]
rs4634864	0.83[ASN][1000 genomes]
rs4642852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4651064	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs4652493	0.85[CHB][hapmap]
rs4652495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652498	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652505	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs55874160	1.00[ASN][1000 genomes]
rs60286873	0.91[ASN][1000 genomes]
rs6425634	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs6657492	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658310	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6659513	1.00[ASN][1000 genomes]
rs6661208	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6665719	0.90[CHB][hapmap]
rs6670544	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6674244	0.82[ASN][1000 genomes]
rs6678216	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697924	0.82[CHB][hapmap]
rs6700986	0.82[ASN][1000 genomes]
rs72720915	0.83[ASN][1000 genomes]
rs72720917	0.83[ASN][1000 genomes]
rs7523003	0.81[ASN][1000 genomes]
rs7523857	0.82[ASN][1000 genomes]
rs7526189	0.93[ASN][1000 genomes]
rs7528650	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs7532806	0.88[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7538219	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538303	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544585	1.00[ASN][1000 genomes]
rs822706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425497	0.94[EUR][1000 genomes]
rs9425878	0.90[EUR][1000 genomes]
rs9425880	0.94[EUR][1000 genomes]
rs9701037	0.84[ASN][1000 genomes]
rs9729819	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
7	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425625	HNMT	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180309600-180345400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:180310000-180348200	Weak transcription	Primary B cells from cord blood	blood
3	chr1:180313400-180335200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:180314000-180345800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:180323600-180332200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:180324000-180341600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:180329000-180334800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:180330200-180332600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:180330200-180334800	Weak transcription	A549	lung
10	chr1:180330200-180335400	Weak transcription	Osteobl	bone
11	chr1:180330200-180338200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:180330200-180345400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:180330400-180335200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:180330400-180335400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:180330400-180335600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:180330600-180349000	Weak transcription	HMEC	breast
17	chr1:180331000-180333000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:180331200-180333200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:180331400-180333000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:180331600-180332800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:180331600-180333200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:180331600-180335400	Weak transcription	HSMM	muscle
23	chr1:180331800-180333200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:180332000-180332800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:180332000-180333000	Enhancers	Ovary	ovary
26	chr1:180332000-180333200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:180332000-180333400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:180332000-180335400	Weak transcription	HSMMtube	muscle

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