Variant report

Variant	rs6685187
Chromosome Location	chr1:151858888-151858889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151856848..151858901-chr1:152006304..152009050,2	K562	blood:
2	chr1:151855508..151860878-chr1:151961893..151967107,7	MCF-7	breast:
3	chr1:151856833..151859482-chr1:151860207..151863814,3	MCF-7	breast:
4	chr1:151857333..151860480-chr1:152007205..152010628,3	MCF-7	breast:
5	chr1:151858557..151860103-chr1:151875689..151877442,2	K562	blood:
6	chr1:151857351..151860092-chr1:151985508..151987866,2	MCF-7	breast:
7	chr1:151858712..151862714-chr1:151863688..151869439,8	K562	blood:
8	chr1:151847463..151849463-chr1:151858810..151860605,2	MCF-7	breast:
9	chr1:151856251..151859847-chr1:151881652..151883718,3	K562	blood:
10	chr1:151851800..151854388-chr1:151856922..151859554,2	K562	blood:
11	chr1:151857196..151858906-chr1:151869023..151871205,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000229021	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1060870	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788817	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]
rs10788818	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10788820	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10888445	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204914	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204915	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12067594	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12116923	0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs12562586	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13320	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1387833	0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs1490189	0.83[AMR][1000 genomes]
rs1907040	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2130525	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2279501	0.81[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2279502	0.81[CEU][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs2338201	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2338209	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2932565	0.84[AMR][1000 genomes]
rs2932576	0.83[AMR][1000 genomes]
rs2932577	0.83[AMR][1000 genomes]
rs2932579	0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs2932583	0.80[AMR][1000 genomes]
rs2932590	0.81[TSI][hapmap]
rs2999506	0.83[AMR][1000 genomes]
rs2999526	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs2999528	0.85[MEX][hapmap];0.82[TSI][hapmap]
rs2999531	0.90[MEX][hapmap]
rs2999534	0.80[MEX][hapmap]
rs2999541	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2999542	0.83[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs2999544	0.83[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs2999545	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2999546	0.83[AMR][1000 genomes]
rs3007670	0.83[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3007685	0.83[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3007691	0.80[AMR][1000 genomes]
rs3007708	0.85[MEX][hapmap]
rs3007711	0.83[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845409	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845713	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6684312	0.95[CHB][hapmap]
rs6698740	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523082	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541453	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7542137	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9435963	0.84[AMR][1000 genomes]
rs9435964	0.84[AMR][1000 genomes]
rs9943281	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[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
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6685187	THEM4	cis	uninvolved skin	skin_eQTL
rs6685187	THEM4	cis	Nerve Tibial	GTEx
rs6685187	THEM4	cis	lymphoblastoid	seeQTL
rs6685187	S100A10	cis	lymphoblastoid	seeQTL
rs6685187	S100A10	cis	Lymphoblastoid	GTEx
rs6685187	S100A10	cis	multi-tissue	Pritchard
rs6685187	THEM4	cis	multi-tissue	Pritchard
rs6685187	THEM4	cis	cerebellum	SCAN
rs6685187	THEM4	cis	Esophagus Muscularis	GTEx
rs6685187	S100A10	cis	cerebellum	SCAN
rs6685187	THEM4	cis	parietal	SCAN
rs6685187	THEM4	cis	normal skin	skin_eQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:151840600-151864600	Weak transcription	NH-A	brain
4	chr1:151841200-151859200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:151841200-151880800	Weak transcription	NHLF	lung
6	chr1:151841400-151860000	Weak transcription	Hela-S3	cervix
7	chr1:151841400-151860200	Weak transcription	Osteobl	bone
8	chr1:151841600-151864000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:151843400-151859600	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:151844000-151860000	Weak transcription	HSMM	muscle
11	chr1:151844000-151864600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:151844200-151859600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:151844200-151860400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:151844400-151866400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
16	chr1:151844600-151863600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:151844600-151864200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:151844800-151863800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:151844800-151864200	Weak transcription	Pancreas	Pancrea
20	chr1:151844800-151870800	Weak transcription	Gastric	stomach
21	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:151845200-151863600	Weak transcription	Fetal Kidney	kidney
24	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:151845800-151859200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:151846000-151861800	Weak transcription	Psoas Muscle	Psoas
27	chr1:151846000-151864200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:151846400-151859600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:151846400-151860000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:151846400-151860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:151846400-151865400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
33	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:151846600-151859400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:151846600-151864800	Weak transcription	Fetal Lung	lung
36	chr1:151846800-151860400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:151846800-151860400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:151846800-151860600	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:151846800-151863000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:151847000-151859200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:151847000-151863800	Weak transcription	Fetal Thymus	thymus
42	chr1:151847000-151865000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:151847000-151869600	Weak transcription	Small Intestine	intestine
44	chr1:151847000-151871000	Weak transcription	Spleen	Spleen
45	chr1:151847200-151860200	Weak transcription	Lung	lung
46	chr1:151847400-151859600	Weak transcription	Left Ventricle	heart
47	chr1:151847400-151860000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:151847400-151860200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:151847400-151870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:151847600-151859400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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