Variant report

Variant	rs6542045
Chromosome Location	chr2:113015512-113015513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:113015196-113015514	MCF10A-Er-Src	breast:	n/a	chr2:113015356-113015367
2	FOS	chr2:113015195-113015532	HUVEC	blood vessel:	n/a	chr2:113015356-113015367

No.	Distal block	Cell Line	Cell type
1	chr2:113010163..113016150-chr2:113027955..113035093,25	K562	blood:
2	chr2:113015323..113017823-chr2:113341414..113343935,3	K562	blood:
3	chr2:113012803..113017644-chr2:113018976..113023020,5	K562	blood:
4	chr2:113015328..113018702-chr2:113341013..113343935,4	K562	blood:
5	chr2:113013729..113015547-chr2:113015611..113017197,2	K562	blood:

Variant related genes	Relation type
ZC3H8	TF binding region
ENSG00000238951	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10167090	0.81[AFR][1000 genomes]
rs10169159	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10175234	0.86[ASN][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10183121	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs10191002	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs10203843	0.91[AFR][1000 genomes]
rs10205038	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10211300	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10439391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11123132	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs11123136	0.81[AFR][1000 genomes]
rs11674953	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11688418	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689487	0.95[ASN][1000 genomes]
rs11691431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11691794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896500	0.91[AFR][1000 genomes]
rs11903741	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11904424	0.83[ASW][hapmap];0.88[AFR][1000 genomes]
rs12464478	0.83[AFR][1000 genomes]
rs12711737	0.99[ASN][1000 genomes]
rs12711738	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]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13387611	0.90[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs34471791	0.81[AFR][1000 genomes]
rs34623958	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4258804	0.87[AFR][1000 genomes]
rs4299347	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4332934	0.93[AFR][1000 genomes]
rs4352239	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4392265	0.90[ASN][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4430968	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4446076	0.90[ASN][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4450607	0.83[AFR][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4522611	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4539797	0.93[AFR][1000 genomes]
rs4542853	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4578863	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4622729	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4849056	0.89[ASN][1000 genomes]
rs4849057	0.98[ASN][1000 genomes]
rs58337061	0.91[AFR][1000 genomes]
rs6542048	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542050	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6706874	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6708164	0.86[AFR][1000 genomes]
rs6716010	0.88[ASN][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6744364	0.81[AFR][1000 genomes]
rs6745942	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs6758110	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6761599	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs71414636	0.81[ASN][1000 genomes]
rs72831684	0.90[ASN][1000 genomes]
rs7557281	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs7564052	0.88[AFR][1000 genomes]
rs7569894	0.86[AFR][1000 genomes]
rs7571435	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7591439	0.90[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7599041	0.81[AFR][1000 genomes]
rs7600338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7601200	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7601888	0.83[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542045	POLR1B	cis	parietal	SCAN
rs6542045	SULT1C4	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113012600-113016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:113012600-113016800	Weak transcription	Fetal Heart	heart
3	chr2:113012600-113017200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113012800-113017000	Weak transcription	Spleen	Spleen
5	chr2:113012800-113017200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:113013000-113015600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:113013000-113016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:113013000-113016800	Weak transcription	Fetal Kidney	kidney
9	chr2:113013000-113017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:113013000-113017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:113013000-113017000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:113013000-113017000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:113013000-113017000	Weak transcription	Fetal Lung	lung
14	chr2:113013000-113017000	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:113013000-113017000	Weak transcription	Psoas Muscle	Psoas
16	chr2:113013000-113017000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:113013000-113017000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:113013000-113017000	Weak transcription	HMEC	breast
19	chr2:113013000-113017000	Weak transcription	NH-A	brain
20	chr2:113013000-113017000	Weak transcription	NHDF-Ad	bronchial
21	chr2:113013000-113017000	Weak transcription	NHEK	skin
22	chr2:113013000-113017000	Weak transcription	NHLF	lung
23	chr2:113013000-113017200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:113013000-113017200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:113013000-113017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:113013000-113017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:113013000-113017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:113013000-113017200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:113013000-113017200	Weak transcription	Pancreas	Pancrea
30	chr2:113013000-113017400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:113013000-113018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:113013000-113018200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:113013200-113016200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:113013200-113016800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:113013200-113016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:113013200-113016800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:113013200-113017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:113013200-113017000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr2:113013200-113017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:113013200-113017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:113013200-113017000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:113013200-113017000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:113013200-113017000	Weak transcription	Liver	Liver
44	chr2:113013200-113017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:113013200-113017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:113013200-113017000	Weak transcription	Left Ventricle	heart
47	chr2:113013200-113017000	Weak transcription	Ovary	ovary
48	chr2:113013200-113017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:113013200-113017200	Weak transcription	Hela-S3	cervix
50	chr2:113013400-113016800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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