Variant report

Variant	rs2070959
Chromosome Location	chr2:234602191-234602192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234602188-234602212	ProgFib	skin:	n/a	n/a
2	TCF12	chr2:234602175-234603879	A549	lung:	n/a	chr2:234603136-234603145

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
2	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
3	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
4	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
5	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:
6	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
7	chr2:234387197..234390730-chr2:234600088..234603557,3	MCF-7	breast:
8	chr2:234355853..234357392-chr2:234601737..234604100,2	MCF-7	breast:

No data

Variant related genes	Relation type
UGT1A6	TF binding region
ENSG00000085982	Chromatin interaction
ENSG00000224814	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10167119	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10168155	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10168333	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10168416	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10173355	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10179094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10189426	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10197460	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10202865	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10203266	0.94[ASN][1000 genomes]
rs10445704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10929302	0.85[CEU][hapmap]
rs1105879	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1105880	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680450	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11692021	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11692664	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695484	0.85[CEU][hapmap]
rs11902131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12615708	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12623271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13002774	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13009407	0.81[CEU][hapmap]
rs13015720	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17862875	0.85[CEU][hapmap]
rs17863787	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs17864701	0.83[CEU][hapmap]
rs2602376	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2741044	0.85[CEU][hapmap]
rs2741045	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap]
rs2741046	0.85[CEU][hapmap]
rs28899170	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs35984508	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806598	0.86[ASN][1000 genomes]
rs4148324	0.95[CEU][hapmap]
rs4148325	0.95[CEU][hapmap]
rs4261716	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4338954	0.94[ASN][1000 genomes]
rs4347832	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4530361	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4553819	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs45615240	0.94[ASN][1000 genomes]
rs6714634	0.85[CEU][hapmap]
rs6722076	0.90[CEU][hapmap]
rs6724485	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6736508	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6736743	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6742078	0.95[CEU][hapmap]
rs6744284	0.90[CEU][hapmap]
rs6753320	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6753569	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6759892	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7349250	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7563561	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7567229	0.81[EUR][1000 genomes]
rs7571915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7577677	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7586110	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7592281	0.87[ASN][1000 genomes]
rs7608175	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs887829	0.95[CEU][hapmap]
rs929596	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking 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	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2070959	ITM2C	cis	cerebellum	SCAN
rs2070959	EFHD1	cis	cerebellum	SCAN
rs2070959	NPPC	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234597800-234608600	Weak transcription	Gastric	stomach
2	chr2:234599400-234608000	Weak transcription	HUVEC	blood vessel
3	chr2:234600200-234602600	Enhancers	A549	lung
4	chr2:234600400-234608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:234600800-234602400	Enhancers	Fetal Kidney	kidney
6	chr2:234600800-234603000	Weak transcription	Right Atrium	heart
7	chr2:234601000-234602400	Weak transcription	Hela-S3	cervix
8	chr2:234601200-234602200	Enhancers	Pancreas	Pancrea
9	chr2:234601400-234602200	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr2:234601400-234602200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:234601400-234603000	Enhancers	Duodenum Mucosa	Duodenum
12	chr2:234601600-234602400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:234601600-234602800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr2:234601600-234603600	Flanking Active TSS	Liver	Liver
15	chr2:234602000-234602200	Flanking Active TSS	Stomach Mucosa	stomach
16	chr2:234602000-234602800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:234602000-234602800	Enhancers	Esophagus	oesophagus
18	chr2:234602000-234603000	Transcr. at gene 5' and 3'	NHEK	skin
19	chr2:234602000-234603200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin

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