Variant report

Variant	rs1490189
Chromosome Location	chr1:151910254-151910255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151906694..151908997-chr1:151910180..151912030,2	K562	blood:
2	chr1:151903334..151906140-chr1:151909030..151911005,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1038747	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10494270	0.95[CHB][hapmap]
rs1060870	0.85[AMR][1000 genomes]
rs10788817	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788818	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10788820	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888445	0.81[CEU][hapmap]
rs11204914	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204915	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204922	0.81[JPT][hapmap]
rs11589720	0.89[ASN][1000 genomes]
rs12067594	0.87[AMR][1000 genomes]
rs12083193	0.82[CHB][hapmap]
rs12116923	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12562586	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1387833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833668	0.91[CHB][hapmap]
rs16833728	0.86[CHB][hapmap]
rs1907040	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2130525	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279501	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2279502	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2337689	0.81[ASN][1000 genomes]
rs2338019	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2338201	0.85[AMR][1000 genomes]
rs2338209	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932565	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932577	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932581	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2932583	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932586	0.91[ASN][1000 genomes]
rs2932590	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2999506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999508	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2999512	0.88[ASN][1000 genomes]
rs2999526	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2999528	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2999531	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2999541	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999542	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999545	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007670	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007685	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007691	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007708	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3007711	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845409	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845713	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587640	0.82[CHB][hapmap]
rs6663064	0.91[CHB][hapmap]
rs6678672	0.82[CHB][hapmap]
rs6685187	0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs6686874	0.91[CHB][hapmap]
rs6698740	0.85[AMR][1000 genomes]
rs7523082	0.81[CEU][hapmap]
rs7535002	0.83[CHB][hapmap]
rs7541099	0.86[CHB][hapmap]
rs7542137	0.87[AMR][1000 genomes]
rs902313	0.86[CHB][hapmap]
rs9435963	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9435964	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9943221	0.95[CHB][hapmap]
rs9943281	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1490189	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs1490189	THEM4	cis	multi-tissue	Pritchard
rs1490189	THEM4	cis	Esophagus Muscularis	GTEx
rs1490189	THEM4	cis	Nerve Tibial	GTEx
rs1490189	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs1490189	S100A10	cis	Lymphoblastoid	GTEx
rs1490189	S100A10	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151907000-151913000	Weak transcription	NHDF-Ad	bronchial
2	chr1:151907000-151914000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:151907000-151917400	Weak transcription	Right Atrium	heart
4	chr1:151907600-151916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:151907800-151913200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:151908000-151912200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:151908000-151913200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:151908000-151913400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:151908000-151913400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:151908000-151913400	Weak transcription	NH-A	brain
11	chr1:151908000-151913400	Weak transcription	NHEK	skin
12	chr1:151908000-151913600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:151908200-151913000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:151908200-151913600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:151908200-151916600	Weak transcription	Placenta	Placenta
16	chr1:151908200-151917000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:151908400-151913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:151909000-151913200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:151909400-151912800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:151909400-151913600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:151909400-151913600	Weak transcription	Ovary	ovary
22	chr1:151909400-151913600	Weak transcription	Stomach Mucosa	stomach
23	chr1:151909400-151913800	Weak transcription	HepG2	liver
24	chr1:151909400-151916800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:151909400-151917000	Weak transcription	Colonic Mucosa	Colon
26	chr1:151909600-151910400	Weak transcription	Fetal Intestine Large	intestine
27	chr1:151909600-151911200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:151909600-151911400	Weak transcription	A549	lung
29	chr1:151909600-151911600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:151909600-151911600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:151909600-151912800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:151909600-151913000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:151909600-151913200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:151909600-151913200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:151909600-151913200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:151909600-151913600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:151909600-151913600	Weak transcription	Fetal Lung	lung
38	chr1:151909600-151913600	Weak transcription	K562	blood
39	chr1:151909600-151917800	Weak transcription	HUVEC	blood vessel
40	chr1:151909800-151913200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:151909800-151913800	Weak transcription	Adipose Nuclei	Adipose
42	chr1:151909800-151916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:151910200-151912000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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