Variant report

Variant	rs12036670
Chromosome Location	chr1:160832861-160832862
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	EP300	chr1:160832426-160832923	GM12878	blood:	n/a	n/a
2	BCLAF1	chr1:160832427-160832904	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:160832426-160832921	GM12878	blood:	n/a	n/a
4	FOS	chr1:160832603-160832865	MCF10A-Er-Src	breast:	n/a	chr1:160832740-160832750 chr1:160832740-160832750
5	POLR2A	chr1:160831743-160832969	HL-60	blood:	n/a	n/a
6	MAX	chr1:160831778-160833081	NB4	blood:	n/a	chr1:160832086-160832095 chr1:160832380-160832389
7	REST	chr1:160831882-160832898	HL-60	blood:	n/a	chr1:160832663-160832673
8	SPI1	chr1:160831681-160832921	HL-60	blood:	n/a	n/a
9	MTA3	chr1:160832411-160832912	GM12878	blood:	n/a	n/a
10	PAX5	chr1:160832336-160832872	GM12878	blood:	n/a	n/a
11	NRF1	chr1:160832458-160832989	GM12878	blood:	n/a	n/a
12	CUX1	chr1:160832566-160832894	GM12878	blood:	n/a	n/a
13	NFIC	chr1:160832369-160832950	GM12878	blood:	n/a	n/a
14	RUNX3	chr1:160832321-160832892	GM12878	blood:	n/a	n/a
15	BATF	chr1:160832529-160832890	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:160831680-160832998	HL-60	blood:	n/a	n/a
17	MAX	chr1:160832164-160832864	GM12878	blood:	n/a	chr1:160832380-160832389

Variant related genes	Relation type
CD244	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10908807	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265498	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11265499	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265500	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265501	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265504	0.93[ASN][1000 genomes]
rs12035295	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12035537	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037740	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12038419	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038600	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039896	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12039959	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12040060	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12040152	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12040750	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041508	0.96[ASN][1000 genomes]
rs12046019	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12046021	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047127	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12048113	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12566557	0.92[ASN][1000 genomes]
rs1412849	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1576964	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1855188	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1855189	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2151293	0.94[ASN][1000 genomes]
rs2184067	0.94[ASN][1000 genomes]
rs2184068	0.93[ASN][1000 genomes]
rs2184069	0.94[ASN][1000 genomes]
rs3766378	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4017448	0.94[ASN][1000 genomes]
rs4017458	0.96[ASN][1000 genomes]
rs4017459	0.92[ASN][1000 genomes]
rs4017460	0.94[ASN][1000 genomes]
rs4656940	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656941	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656944	0.96[ASN][1000 genomes]
rs4656945	0.96[ASN][1000 genomes]
rs4656948	0.91[ASN][1000 genomes]
rs4656949	0.93[ASN][1000 genomes]
rs4656950	0.94[ASN][1000 genomes]
rs57483437	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58418513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59712018	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803263	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61803285	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6676174	0.94[ASN][1000 genomes]
rs6685693	0.93[ASN][1000 genomes]
rs6698454	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6699162	0.93[ASN][1000 genomes]
rs6699166	0.94[ASN][1000 genomes]
rs6700146	0.94[ASN][1000 genomes]
rs72710762	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7410867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412693	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7412696	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7414728	0.94[ASN][1000 genomes]
rs7419088	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7419110	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7419145	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs869167	0.93[ASN][1000 genomes]
rs869168	0.94[ASN][1000 genomes]
rs914793	0.92[ASN][1000 genomes]
rs952804	0.94[ASN][1000 genomes]
rs955370	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959047	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12036670	RHBG	cis	parietal	SCAN
rs12036670	PPOX	cis	cerebellum	SCAN
rs12036670	DEDD	cis	cerebellum	SCAN
rs12036670	CD5L	cis	parietal	SCAN
rs12036670	RXFP4	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160828600-160835000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:160830000-160833000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr1:160830000-160833200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:160830000-160833800	Enhancers	Primary B cells from cord blood	blood
5	chr1:160830200-160834200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:160830600-160833000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:160830600-160833000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:160830600-160833600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr1:160831200-160833600	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:160831800-160833000	Enhancers	Primary T cells from cord blood	blood
11	chr1:160831800-160833000	Enhancers	Fetal Heart	heart
12	chr1:160831800-160834400	Enhancers	GM12878-XiMat	blood
13	chr1:160832200-160833000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:160832200-160833000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:160832200-160837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:160832400-160833000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:160832400-160833000	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr1:160832400-160833000	Enhancers	Fetal Intestine Small	intestine
19	chr1:160832400-160833000	Enhancers	Right Ventricle	heart
20	chr1:160832400-160833800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:160832400-160834000	Enhancers	Fetal Thymus	thymus
22	chr1:160832600-160833000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:160832600-160833000	Enhancers	Colonic Mucosa	Colon
24	chr1:160832600-160835400	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:160832600-160835400	Weak transcription	Liver	Liver
26	chr1:160832600-160835400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:160832600-160835400	Weak transcription	Right Atrium	heart
28	chr1:160832600-160835600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:160832600-160847400	Weak transcription	Spleen	Spleen
30	chr1:160832800-160833000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr1:160832800-160833200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr1:160832800-160833200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:160832800-160833800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:160832800-160834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:160832800-160834000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:160832800-160834000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:160832800-160834600	Enhancers	Ovary	ovary

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