Variant report

Variant	rs6667498
Chromosome Location	chr1:146708029-146708030
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146694787..146699847-chr1:146706639..146711306,10	MCF-7	breast:
2	chr1:146624878..146626860-chr1:146707008..146708792,2	K562	blood:
3	chr1:146642343..146646438-chr1:146707270..146711599,11	MCF-7	breast:
4	chr1:146656864..146658440-chr1:146707993..146710548,2	MCF-7	breast:
5	chr1:146642484..146645214-chr1:146706484..146708315,2	K562	blood:
6	chr1:146704247..146709929-chr1:146710011..146715268,7	K562	blood:
7	chr1:146638044..146647556-chr1:146707628..146717159,48	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131781	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000236806	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000131778	Chromatin interaction
ENSG00000271721	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10751403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751404	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751414	1.00[EUR][1000 genomes]
rs10793659	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793666	1.00[EUR][1000 genomes]
rs10900323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900324	1.00[ASN][1000 genomes]
rs10900331	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs10900334	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239952	0.94[EUR][1000 genomes]
rs1372819	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442759	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530335	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1530336	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1530337	1.00[ASN][1000 genomes]
rs1561879	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822306	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1822311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890036	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890039	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1899484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932982	1.00[EUR][1000 genomes]
rs2120004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120005	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354433	1.00[ASN][1000 genomes]
rs2354434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs41295831	1.00[EUR][1000 genomes]
rs4245679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534444	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4950310	1.00[ASN][1000 genomes]
rs4950381	1.00[ASN][1000 genomes]
rs4950385	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4950386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950407	1.00[EUR][1000 genomes]
rs56859828	1.00[ASN][1000 genomes]
rs571183	1.00[ASN][1000 genomes]
rs572109	1.00[ASN][1000 genomes]
rs6593746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593747	1.00[ASN][1000 genomes]
rs6593753	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593754	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593768	1.00[EUR][1000 genomes]
rs6681716	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6682309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683215	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692455	0.88[EUR][1000 genomes]
rs6697092	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6703847	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs72999607	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999651	1.00[ASN][1000 genomes]
rs7517150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7523954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531878	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535052	1.00[EUR][1000 genomes]
rs7535394	1.00[ASN][1000 genomes]
rs7537279	1.00[ASN][1000 genomes]
rs7546434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7547279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552601	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553584	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7555913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs894469	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs894470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs894471	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs894472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920682	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
26	nsv872258	chr1:146662018-146709784	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
27	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
28	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6667498	FMO5	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146705800-146708600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr1:146705800-146708800	Enhancers	Liver	Liver
3	chr1:146705800-146709200	Enhancers	HepG2	liver
4	chr1:146705800-146710600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:146705800-146711600	Enhancers	Stomach Mucosa	stomach
6	chr1:146707400-146708600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr1:146707400-146709400	Enhancers	Pancreas	Pancrea
8	chr1:146707600-146708600	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:146707600-146708800	Enhancers	Colonic Mucosa	Colon
10	chr1:146707600-146708800	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr1:146707600-146709200	Enhancers	Gastric	stomach
12	chr1:146707600-146709200	Enhancers	Lung	lung
13	chr1:146707600-146709400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:146707600-146709400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:146707600-146713000	Enhancers	Fetal Intestine Large	intestine
16	chr1:146707800-146708800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr1:146707800-146709000	Enhancers	Small Intestine	intestine

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