Variant report

Variant	rs12040750
Chromosome Location	chr1:160833805-160833806
allele	G/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	SPI1	chr1:160833515-160833859	GM12878	blood:	n/a	chr1:160833722-160833731
2	CTCF	chr1:160833760-160833910	HepG2	liver:	n/a	n/a
3	SPI1	chr1:160833203-160833915	HL-60	blood:	n/a	chr1:160833722-160833731 chr1:160833456-160833463 chr1:160833454-160833467
4	SPI1	chr1:160833581-160833846	GM12891	blood:	n/a	chr1:160833722-160833731
5	POLR2A	chr1:160833084-160834145	K562	blood:	n/a	n/a
6	RAD21	chr1:160833678-160833929	H1-hESC	embryonic stem cell:	n/a	chr1:160833797-160833810 chr1:160833799-160833811 chr1:160833799-160833809
7	SPI1	chr1:160833534-160833857	GM12891	blood:	n/a	chr1:160833722-160833731

Variant related genes	Relation type
CD244	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10908807	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265498	0.93[EUR][1000 genomes]
rs11265499	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265500	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265501	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265504	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12035295	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12035537	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036607	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12036670	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037395	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037740	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12037885	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12038419	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039896	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039959	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12040060	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12040152	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12041508	0.96[ASN][1000 genomes]
rs12046019	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12046021	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047127	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12048113	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12566557	0.92[ASN][1000 genomes]
rs1412849	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1576964	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1855188	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1855189	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2151293	0.94[ASN][1000 genomes]
rs2184067	0.94[ASN][1000 genomes]
rs2184068	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2184069	0.94[ASN][1000 genomes]
rs4017448	0.94[ASN][1000 genomes]
rs4017458	0.96[ASN][1000 genomes]
rs4017459	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4017460	0.94[ASN][1000 genomes]
rs4656940	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656941	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656943	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656944	0.96[ASN][1000 genomes]
rs4656945	0.96[ASN][1000 genomes]
rs4656948	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4656949	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4656950	0.94[ASN][1000 genomes]
rs57483437	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58418513	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59712018	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803263	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61803285	0.80[AFR][1000 genomes];0.98[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	0.80[AFR][1000 genomes];0.98[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	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7410867	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412693	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7412696	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7414728	0.94[ASN][1000 genomes]
rs7419088	0.93[EUR][1000 genomes]
rs7419110	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7419145	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs869167	0.93[ASN][1000 genomes]
rs869168	0.94[ASN][1000 genomes]
rs914793	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs952804	0.94[ASN][1000 genomes]
rs955370	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955371	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12040750	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160828600-160835000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:160830200-160834200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:160831800-160834400	Enhancers	GM12878-XiMat	blood
4	chr1:160832200-160837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:160832400-160834000	Enhancers	Fetal Thymus	thymus
6	chr1:160832600-160835400	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:160832600-160835400	Weak transcription	Liver	Liver
8	chr1:160832600-160835400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:160832600-160835400	Weak transcription	Right Atrium	heart
10	chr1:160832600-160835600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:160832600-160847400	Weak transcription	Spleen	Spleen
12	chr1:160832800-160834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:160832800-160834000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:160832800-160834000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:160832800-160834600	Enhancers	Ovary	ovary
16	chr1:160833000-160834000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:160833000-160834600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:160833000-160834800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:160833000-160835400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:160833600-160834400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160833600-160840000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:160833800-160834000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:160833800-160834000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:160833800-160837400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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