Variant report

Variant	rs4656943
Chromosome Location	chr1:160833526-160833527
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	SPI1	chr1:160833093-160833757	GM12878	blood:	n/a	chr1:160833722-160833731 chr1:160833456-160833463 chr1:160833454-160833467
2	SPI1	chr1:160833515-160833859	GM12878	blood:	n/a	chr1:160833722-160833731
3	SPI1	chr1:160833251-160833726	HL-60	blood:	n/a	chr1:160833456-160833463 chr1:160833454-160833467
4	SPI1	chr1:160833400-160833527	K562	blood:	n/a	chr1:160833456-160833463 chr1:160833454-160833467
5	SPI1	chr1:160833203-160833915	HL-60	blood:	n/a	chr1:160833722-160833731 chr1:160833456-160833463 chr1:160833454-160833467
6	SPI1	chr1:160833281-160833574	GM12891	blood:	n/a	chr1:160833456-160833463 chr1:160833454-160833467
7	POLR2A	chr1:160833084-160834145	K562	blood:	n/a	n/a

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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265498	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs11265499	0.81[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];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265501	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265504	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12035295	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12035537	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036607	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12036670	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]
rs12037395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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]
rs12037740	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12037885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12038419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038600	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039896	0.91[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039959	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12040060	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12040152	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12040750	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041508	0.96[ASN][1000 genomes]
rs12046019	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12046021	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047127	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12048113	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12566557	0.92[ASN][1000 genomes]
rs1412849	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1576964	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1855188	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1855189	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2151293	0.94[ASN][1000 genomes]
rs2184067	0.94[ASN][1000 genomes]
rs2184068	0.84[AFR][1000 genomes];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	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4017460	0.94[ASN][1000 genomes]
rs4656940	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656941	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656944	0.96[ASN][1000 genomes]
rs4656945	0.96[ASN][1000 genomes]
rs4656948	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4656949	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4656950	0.94[ASN][1000 genomes]
rs57483437	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58418513	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59712018	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803263	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61803285	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6676174	0.94[ASN][1000 genomes]
rs6685693	0.93[ASN][1000 genomes]
rs6698454	0.97[AMR][1000 genomes];0.96[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	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7410867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs7412693	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7412696	0.82[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];0.93[EUR][1000 genomes]
rs7419110	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7419145	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs869167	0.93[ASN][1000 genomes]
rs869168	0.94[ASN][1000 genomes]
rs914793	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs952804	0.94[ASN][1000 genomes]
rs955370	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];1.00[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
rs4656943	DEDD	cis	cerebellum	SCAN
rs4656943	RXFP4	cis	parietal	SCAN
rs4656943	PPOX	cis	cerebellum	SCAN
rs4656943	CD5L	cis	parietal	SCAN
rs4656943	RHBG	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160828600-160835000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:160830000-160833800	Enhancers	Primary B cells from cord blood	blood
3	chr1:160830200-160834200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:160830600-160833600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr1:160831200-160833600	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:160831800-160834400	Enhancers	GM12878-XiMat	blood
7	chr1:160832200-160837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:160832400-160833800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:160832400-160834000	Enhancers	Fetal Thymus	thymus
10	chr1:160832600-160835400	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:160832600-160835400	Weak transcription	Liver	Liver
12	chr1:160832600-160835400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:160832600-160835400	Weak transcription	Right Atrium	heart
14	chr1:160832600-160835600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:160832600-160847400	Weak transcription	Spleen	Spleen
16	chr1:160832800-160833800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:160832800-160834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:160832800-160834000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:160832800-160834000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:160832800-160834600	Enhancers	Ovary	ovary
21	chr1:160833000-160833800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:160833000-160834000	Weak transcription	Fetal Intestine Small	intestine
23	chr1:160833000-160834600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:160833000-160834800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr1:160833000-160835400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:160833200-160833600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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