Variant report

Variant	rs10788817
Chromosome Location	chr1:151882856-151882857
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151881809-151883419	K562	blood:	n/a	n/a
2	HCFC1	chr1:151881417-151883304	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr1:151881486-151883036	K562	blood:	n/a	n/a
4	POLR2A	chr1:151881528-151882900	K562	blood:	n/a	n/a
5	MAFF	chr1:151882499-151882865	K562	blood:	n/a	n/a
6	MAZ	chr1:151881392-151882866	IMR90	lung:	n/a	n/a
7	GABPA	chr1:151881393-151882986	MCF-7	breast:	n/a	n/a
8	MXI1	chr1:151881157-151883004	IMR90	lung:	n/a	chr1:151882314-151882323
9	POLR2A	chr1:151881479-151882992	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:151879473-151883028	K562	blood:	n/a	n/a
11	POLR2A	chr1:151881608-151882893	K562	blood:	n/a	n/a
12	BACH1	chr1:151882789-151882965	K562	blood:	n/a	n/a
13	POLR2A	chr1:151881381-151882890	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:151881490-151882856	HepG2	liver:	n/a	n/a
15	NR2F2	chr1:151881351-151882938	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:151881069-151883044	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:151881587-151883266	PANC-1	pancreas:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:
2	chr1:151882662..151885279-chr19:12903227..12904893,2	MCF-7	breast:
3	chr1:151881661..151883557-chr1:152019981..152021490,2	K562	blood:
4	chr1:151863646..151865677-chr1:151881470..151883641,2	K562	blood:
5	chr1:151879131..151885542-chr1:151961269..151968730,13	MCF-7	breast:
6	chr1:151877897..151883557-chr1:152019456..152022411,7	K562	blood:
7	chr1:151880209..151887387-chr1:151961986..151968084,15	MCF-7	breast:
8	chr1:151880619..151883226-chr1:151961289..151965303,4	K562	blood:
9	chr1:151881708..151882900-chr15:59041095..59042389,4	Hela-S3	cervix:
10	chr1:151879353..151883785-chr1:152005989..152009719,8	K562	blood:
11	chr1:151879656..151883388-chr1:152007614..152010954,7	K562	blood:
12	chr1:151810931..151813859-chr1:151881520..151883452,3	MCF-7	breast:
13	chr1:151882722..151885720-chr1:151898176..151900104,2	MCF-7	breast:

No data

Variant related genes	Relation type
THEM4	TF binding region
ENSG00000163191	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1038747	0.83[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10494270	0.90[CHB][hapmap]
rs1060870	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10788818	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788820	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888445	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204922	0.81[JPT][hapmap]
rs11589720	0.86[ASN][1000 genomes]
rs12067594	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12116923	0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12562586	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13320	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1387833	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1490189	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833668	0.86[CHB][hapmap]
rs16833728	0.81[CHB][hapmap]
rs1907040	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2130525	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279501	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279502	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2338019	0.82[JPT][hapmap]
rs2338201	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2338209	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932565	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932576	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932577	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932579	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932581	0.84[ASN][1000 genomes]
rs2932583	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2932586	0.87[ASN][1000 genomes]
rs2932590	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2999506	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999508	0.84[ASN][1000 genomes]
rs2999512	0.84[ASN][1000 genomes]
rs2999526	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2999528	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2999531	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2999541	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999545	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999546	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007691	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3007708	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3007711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845409	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6663064	0.86[CHB][hapmap]
rs6685187	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6686874	0.86[CHB][hapmap]
rs6698740	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7523082	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7541099	0.81[CHB][hapmap]
rs7541453	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7542137	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs902313	0.81[CHB][hapmap]
rs9435963	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9435964	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9943221	0.91[CHB][hapmap]
rs9943281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Serum metabolite levels	24625756	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10788817	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs10788817	THEM4	cis	Nerve Tibial	GTEx
rs10788817	S100A10	cis	Lymphoblastoid	GTEx
rs10788817	THEM4	cis	uninvolved skin	skin_eQTL
rs10788817	S100A10	cis	multi-tissue	Pritchard
rs10788817	THEM4	cis	Esophagus Muscularis	GTEx
rs10788817	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs10788817	THEM4	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151880400-151883000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:151880600-151883400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:151881000-151883000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:151881000-151883000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:151881000-151883000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:151881000-151883000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:151881000-151883000	Active TSS	GM12878-XiMat	blood
8	chr1:151881000-151883400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:151881200-151883000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:151881200-151883000	Active TSS	Aorta	Aorta
11	chr1:151881200-151883000	Active TSS	Fetal Intestine Large	intestine
12	chr1:151881200-151883000	Active TSS	Psoas Muscle	Psoas
13	chr1:151881200-151883000	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:151881200-151883000	Active TSS	A549	lung
15	chr1:151881200-151883000	Active TSS	HSMM	muscle
16	chr1:151881200-151883000	Active TSS	NHDF-Ad	bronchial
17	chr1:151881400-151883000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:151881400-151883000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:151881600-151883000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:151881600-151883000	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:151881600-151883000	Active TSS	Left Ventricle	heart
22	chr1:151882000-151883000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:151882000-151883000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:151882400-151883000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:151882400-151883000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151882400-151883000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:151882400-151883000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:151882400-151883000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:151882400-151883000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr1:151882400-151883000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr1:151882400-151883000	Flanking Active TSS	Osteobl	bone
32	chr1:151882400-151883200	Flanking Active TSS	Liver	Liver
33	chr1:151882400-151883200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:151882600-151883000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:151882600-151883000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:151882600-151883000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:151882600-151883000	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr1:151882600-151883000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:151882600-151883000	Flanking Active TSS	Fetal Heart	heart
40	chr1:151882600-151883000	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr1:151882600-151883000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr1:151882600-151883000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr1:151882600-151883000	Flanking Active TSS	HepG2	liver
44	chr1:151882600-151883200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:151882600-151883200	Flanking Active TSS	Hela-S3	cervix
46	chr1:151882600-151883200	Flanking Active TSS	K562	blood
47	chr1:151882600-151883400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:151882800-151883000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:151882800-151883000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:151882800-151883000	Enhancers	Primary hematopoietic stem cells	blood

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