Variant report

Variant	rs3738590
Chromosome Location	chr1:155630752-155630753
allele	C/T
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	POLR2A	chr1:155629289-155630863	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:155630346-155630770	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:155629464-155630786	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155619365..155621539-chr1:155630413..155632008,2	K562	blood:

Variant related genes	Relation type
ENSG00000246203	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10908469	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs10908470	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10908471	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10908472	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10908479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908481	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs10908482	0.82[ASN][1000 genomes]
rs11264380	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11264381	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264383	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264386	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11264387	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11264393	0.93[EUR][1000 genomes]
rs11264397	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264398	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264409	0.82[ASN][1000 genomes]
rs12022088	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030596	0.86[EUR][1000 genomes]
rs12035524	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12039893	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040100	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047626	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12047756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12079134	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12093350	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12143948	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12724079	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12740629	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12744132	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12746592	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12758945	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360554	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs1556488	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs2048431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2175391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28662267	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34124416	0.94[EUR][1000 genomes]
rs34620961	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348186	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348196	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35615695	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3820594	0.92[CEU][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs3851912	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3892792	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4278368	0.83[ASN][1000 genomes]
rs4550031	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs475550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs490608	0.85[ASN][1000 genomes]
rs4971095	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427278	0.89[EUR][1000 genomes]
rs6427286	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6427287	0.81[ASN][1000 genomes]
rs644853	0.91[JPT][hapmap]
rs6665227	0.82[ASN][1000 genomes]
rs6672128	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6688636	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs6696888	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs670876	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs678157	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs708611	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs7411786	0.84[EUR][1000 genomes]
rs7521594	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541060	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7550402	0.81[ASN][1000 genomes]
rs821551	0.91[JPT][hapmap]
rs822490	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs860295	0.84[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs9426933	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3738590	GPATCH4	cis	parietal	SCAN
rs3738590	THEM5	cis	parietal	SCAN
rs3738590	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs3738590	FDPS	cis	parietal	SCAN
rs3738590	YY1AP1	cis	parietal	SCAN
rs3738590	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs3738590	RIT1	cis	cerebellum	SCAN
rs3738590	YY1AP1	cis	cerebellum	SCAN
rs3738590	SPRR2A	cis	cerebellum	SCAN
rs3738590	SPRR2B	cis	parietal	SCAN
rs3738590	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155617800-155637000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:155618800-155631800	Weak transcription	K562	blood
3	chr1:155625600-155635400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:155626600-155641800	Weak transcription	Fetal Heart	heart
5	chr1:155627000-155641000	Strong transcription	Fetal Stomach	stomach
6	chr1:155627000-155657600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:155627200-155636800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:155627200-155639600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:155627200-155640800	Strong transcription	Thymus	Thymus
10	chr1:155627200-155641000	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:155627200-155648200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:155627200-155651600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:155627200-155654000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:155627400-155634600	Strong transcription	Primary B cells from cord blood	blood
15	chr1:155627400-155635800	Weak transcription	Fetal Kidney	kidney
16	chr1:155627600-155631000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:155627600-155632400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:155627600-155650200	Strong transcription	GM12878-XiMat	blood
19	chr1:155627600-155650600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:155627600-155653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:155627800-155650600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:155628000-155630800	Strong transcription	Brain Germinal Matrix	brain
23	chr1:155628000-155631200	Strong transcription	HUVEC	blood vessel
24	chr1:155628000-155632200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:155628000-155632800	Strong transcription	HSMM	muscle
26	chr1:155628000-155633000	Strong transcription	Esophagus	oesophagus
27	chr1:155628000-155639400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:155628000-155641000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:155628000-155641200	Strong transcription	Fetal Intestine Small	intestine
30	chr1:155628000-155641400	Strong transcription	Liver	Liver
31	chr1:155628000-155647600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:155628000-155648000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:155628000-155650400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:155628000-155650400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:155628000-155650400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:155628000-155650600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:155628000-155650600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:155628000-155650600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:155628000-155650600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:155628000-155650800	Strong transcription	Primary T cells from cord blood	blood
41	chr1:155628000-155650800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:155628000-155650800	Strong transcription	Placenta	Placenta
43	chr1:155628000-155651600	Strong transcription	Adipose Nuclei	Adipose
44	chr1:155628000-155652000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:155628000-155652000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:155628000-155653800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:155628000-155654600	Strong transcription	Fetal Thymus	thymus
48	chr1:155628200-155631000	Strong transcription	HMEC	breast
49	chr1:155628200-155631400	Strong transcription	HepG2	liver
50	chr1:155628200-155632600	Strong transcription	HSMMtube	muscle

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