Variant report

Variant	rs12711738
Chromosome Location	chr2:113030784-113030785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:113029639-113031158	K562	blood:	n/a	n/a
2	CUX1	chr2:113030202-113030856	K562	blood:	n/a	n/a
3	TEAD4	chr2:113030107-113030833	K562	blood:	n/a	n/a
4	RCOR1	chr2:113030359-113030862	K562	blood:	n/a	n/a
5	UBTF	chr2:113030334-113030835	K562	blood:	n/a	n/a
6	TBL1XR1	chr2:113030047-113030862	K562	blood:	n/a	n/a
7	ZMIZ1	chr2:113030257-113031034	K562	blood:	n/a	n/a
8	CCNT2	chr2:113030275-113030910	K562	blood:	n/a	n/a
9	POLR2A	chr2:113030293-113030807	K562	blood:	n/a	n/a
10	ZNF384	chr2:113030208-113034002	K562	blood:	n/a	n/a
11	GATA1	chr2:113029747-113031594	K562	blood:	n/a	n/a
12	UBTF	chr2:113030451-113031175	K562	blood:	n/a	n/a
13	POLR2A	chr2:113030778-113031677	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr2:113030266-113030837	K562	blood:	n/a	n/a
15	IRF1	chr2:113029973-113031927	K562	blood:	n/a	n/a
16	POLR2A	chr2:113030196-113032194	K562	blood:	n/a	n/a
17	IRF1	chr2:113030256-113032085	K562	blood:	n/a	n/a
18	POLR2A	chr2:113030744-113030869	HepG2	liver:	n/a	n/a
19	GATA1	chr2:113030158-113031322	PBDE	blood:	n/a	n/a
20	MAZ	chr2:113030163-113031058	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113008666..113014085-chr2:113030385..113035561,7	MCF-7	breast:
2	chr14:65875763..65877447-chr2:113029987..113031986,2	MCF-7	breast:
3	chr2:113010163..113016150-chr2:113027955..113035093,25	K562	blood:

No data

Variant related genes	Relation type
ZC3H6	TF binding region
ENSG00000238951	TF binding region
ENSG00000033170	Chromatin interaction
ENSG00000144161	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10167090	0.83[ASN][1000 genomes]
rs10169159	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175234	0.91[ASN][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10183121	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs10191002	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs10196933	0.81[ASN][1000 genomes]
rs10203614	0.81[ASN][1000 genomes]
rs10203843	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10205038	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10211300	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10439391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11123131	0.82[ASN][1000 genomes]
rs11123132	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs11123135	0.81[ASN][1000 genomes]
rs11674953	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11688418	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11689487	0.99[ASN][1000 genomes]
rs11691431	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11691794	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896500	0.86[AFR][1000 genomes]
rs11903741	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11904424	0.83[ASW][hapmap];0.83[AFR][1000 genomes]
rs12620553	0.81[ASN][1000 genomes]
rs12711737	0.93[ASN][1000 genomes]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13387611	0.90[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs13407329	0.82[ASN][1000 genomes]
rs34623958	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258804	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4299347	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4332934	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4352239	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4392265	0.96[ASN][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4419238	0.81[ASN][1000 genomes]
rs4430968	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4446076	0.96[ASN][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4522611	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4539797	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4542853	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4578863	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4622729	0.91[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4849056	0.87[ASN][1000 genomes]
rs4849057	0.92[ASN][1000 genomes]
rs58337061	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6542045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542048	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542050	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6706874	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708164	0.81[AFR][1000 genomes]
rs6716010	0.94[ASN][1000 genomes]
rs6725933	0.81[ASN][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6745942	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6758110	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs6761599	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs71414636	0.87[ASN][1000 genomes]
rs72831684	0.96[ASN][1000 genomes]
rs7557281	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7564052	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7569894	0.81[AFR][1000 genomes]
rs7571435	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7591439	0.90[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7600338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7601200	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7601888	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers 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	33 gene(s)	inside rSNPs	diseases
15	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12711738	POLR1B	cis	parietal	SCAN
rs12711738	SULT1C4	cis	cerebellum	SCAN
rs12711738	ZC3H6	cis	multi-tissue	Pritchard
rs12711738	MERTK	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113025200-113032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:113026400-113032200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:113026800-113032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:113029200-113031200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:113029400-113032200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:113030000-113031600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:113030200-113031400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:113030200-113031400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:113030200-113032000	Weak transcription	HepG2	liver
10	chr2:113030400-113031400	Flanking Active TSS	K562	blood
11	chr2:113030600-113032200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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