Variant report

Variant	rs1019842
Chromosome Location	chr2:128305196-128305197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10177052	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1075774	0.85[CEU][hapmap]
rs10803587	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs10803589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11673952	0.86[CEU][hapmap]
rs11679414	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11683986	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11691916	1.00[ASN][1000 genomes]
rs11692990	1.00[ASN][1000 genomes]
rs12621149	0.81[CEU][hapmap]
rs13030463	1.00[ASN][1000 genomes]
rs13425641	0.87[AMR][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1549767	0.80[CEU][hapmap]
rs1568278	1.00[ASN][1000 genomes]
rs17261845	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17261859	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1820969	1.00[ASN][1000 genomes]
rs1864552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864554	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052954	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069895	1.00[ASN][1000 genomes]
rs2069898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069902	1.00[ASN][1000 genomes]
rs2069904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2069919	1.00[ASN][1000 genomes]
rs2099210	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2163345	1.00[ASN][1000 genomes]
rs2163348	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334138	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334154	0.88[EUR][1000 genomes]
rs334156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334157	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334158	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893897	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662736	1.00[ASN][1000 genomes]
rs4662741	0.86[CEU][hapmap]
rs55998444	1.00[ASN][1000 genomes]
rs5937	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs59378658	1.00[ASN][1000 genomes]
rs6430938	1.00[ASN][1000 genomes]
rs6706077	0.86[CEU][hapmap]
rs6709113	0.86[CEU][hapmap]
rs6722447	0.81[CEU][hapmap]
rs6756535	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72845991	1.00[ASN][1000 genomes]
rs72845993	1.00[ASN][1000 genomes]
rs72845997	1.00[ASN][1000 genomes]
rs72846002	1.00[ASN][1000 genomes]
rs72848604	1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	1.00[ASN][1000 genomes]
rs72848616	1.00[ASN][1000 genomes]
rs72848618	1.00[ASN][1000 genomes]
rs7562428	1.00[ASN][1000 genomes]
rs7582598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592490	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7600934	0.86[CEU][hapmap]
rs7607907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs777569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891514	0.86[CEU][hapmap]
rs9287540	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv2912	chr2:128281152-128307830	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv998519	chr2:128292190-128352032	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008180	chr2:128295320-128355891	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1005109	chr2:128295320-128363255	Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001939	chr2:128295320-128363608	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1015051	chr2:128295320-128372079	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1011937	chr2:128295320-128405921	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1008294	chr2:128295320-128420654	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1007207	chr2:128295320-128429775	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS 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	11 gene(s)	inside rSNPs	diseases
11	nsv1003004	chr2:128295320-128474326	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv1013998	chr2:128299079-128355891	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1005799	chr2:128299079-128363255	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1013925	chr2:128299079-128363648	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1001780	chr2:128299079-128364126	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv999302	chr2:128299079-128372079	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1008457	chr2:128299079-128405921	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv1009514	chr2:128299079-128420654	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv1006421	chr2:128299079-128473079	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
20	nsv1004877	chr2:128299079-128479640	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
21	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019842	POLR2D	cis	cerebellum	SCAN
rs1019842	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128284600-128321200	Weak transcription	Spleen	Spleen
2	chr2:128285400-128306600	Weak transcription	Right Atrium	heart
3	chr2:128300200-128320600	Weak transcription	Colonic Mucosa	Colon
4	chr2:128300600-128307200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:128301400-128317000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:128303600-128305400	Strong transcription	Fetal Intestine Large	intestine
7	chr2:128304800-128305200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:128304800-128307200	Weak transcription	Fetal Intestine Small	intestine

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