Variant report

Variant	rs10782004
Chromosome Location	chr16:31363417-31363418
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	POLR2A	chr16:31363180-31364269	HL-60	blood:	n/a	n/a
2	STAT5A	chr16:31362602-31363585	GM12878	blood:	n/a	chr16:31362937-31362949
3	EP300	chr16:31362760-31364050	GM12878	blood:	n/a	chr16:31363039-31363053 chr16:31363907-31363921 chr16:31363095-31363109 chr16:31363944-31363953 chr16:31362909-31362923
4	RUNX3	chr16:31362721-31363433	GM12878	blood:	n/a	n/a
5	MTA3	chr16:31362746-31363503	GM12878	blood:	n/a	n/a
6	RCOR1	chr16:31362750-31363498	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr16:31362803-31363946	GM12878	blood:	n/a	n/a
8	MTA3	chr16:31362555-31364103	GM12878	blood:	n/a	n/a
9	EBF1	chr16:31362788-31363629	GM12878	blood:	n/a	chr16:31363365-31363376
10	MAFK	chr16:31363376-31363542	K562	blood:	n/a	chr16:31363396-31363405 chr16:31363395-31363409
11	CHD2	chr16:31362893-31363684	GM12878	blood:	n/a	n/a
12	ELF1	chr16:31362690-31363523	GM12878	blood:	n/a	n/a
13	SPI1	chr16:31363282-31364268	HL-60	blood:	n/a	chr16:31363943-31363956 chr16:31363911-31363920 chr16:31363944-31363953 chr16:31363613-31363620 chr16:31363909-31363922 chr16:31363945-31363952 chr16:31363942-31363955
14	BRCA1	chr16:31363372-31363541	GM12878	blood:	n/a	n/a
15	NFIC	chr16:31362620-31364115	GM12878	blood:	n/a	n/a
16	PML	chr16:31362618-31363884	GM12878	blood:	n/a	n/a
17	EBF1	chr16:31362742-31363589	GM12878	blood:	n/a	chr16:31363365-31363376
18	ATF2	chr16:31362642-31363600	GM12878	blood:	n/a	n/a
19	POLR2A	chr16:31363049-31364141	GM12892	blood:	n/a	n/a
20	SPI1	chr16:31362657-31364318	GM12878	blood:	n/a	chr16:31362940-31362947 chr16:31363943-31363956 chr16:31363911-31363920 chr16:31364298-31364311 chr16:31363944-31363953 chr16:31363613-31363620 chr16:31363909-31363922 chr16:31363945-31363952 chr16:31363942-31363955 chr16:31362936-31362949

Variant related genes	Relation type
ITGAX	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10747210	0.98[ASN][1000 genomes]
rs1106398	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11150610	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11150611	0.97[ASN][1000 genomes]
rs11150612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11150613	0.93[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11150614	0.85[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11150616	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11150617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11150619	0.88[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1143682	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11574630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574631	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11574639	0.82[ASN][1000 genomes]
rs11641202	0.84[ASN][1000 genomes]
rs11642120	0.84[ASN][1000 genomes]
rs11645917	0.97[ASN][1000 genomes]
rs11859274	0.97[ASN][1000 genomes]
rs11863627	0.84[ASN][1000 genomes]
rs12444713	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12597154	0.87[ASN][1000 genomes]
rs12600286	0.94[ASN][1000 genomes]
rs12923297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12935192	0.97[ASN][1000 genomes]
rs13332545	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13338928	0.87[ASN][1000 genomes]
rs2230429	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2359661	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs28372932	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3087796	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs36100148	0.89[ASN][1000 genomes]
rs3925074	0.92[ASN][1000 genomes]
rs3925075	0.92[ASN][1000 genomes]
rs4075052	0.92[ASN][1000 genomes]
rs4077810	0.92[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs41440449	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4261553	0.92[ASN][1000 genomes]
rs4359460	0.92[ASN][1000 genomes]
rs4411512	0.92[ASN][1000 genomes]
rs4448960	0.92[ASN][1000 genomes]
rs4450409	0.84[ASN][1000 genomes]
rs4459557	0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4493054	0.98[ASN][1000 genomes]
rs4506917	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4594268	0.84[ASN][1000 genomes]
rs4597342	0.92[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4608351	0.92[ASN][1000 genomes]
rs4889543	0.88[ASN][1000 genomes]
rs4889647	0.85[ASN][1000 genomes]
rs4889649	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55742763	0.88[ASN][1000 genomes]
rs55912556	0.83[ASN][1000 genomes]
rs56392848	0.97[ASN][1000 genomes]
rs57202326	0.84[ASN][1000 genomes]
rs59338016	0.88[ASN][1000 genomes]
rs61194152	0.93[ASN][1000 genomes]
rs62051517	0.89[ASN][1000 genomes]
rs7190997	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7192161	0.85[ASN][1000 genomes]
rs7192375	0.87[ASN][1000 genomes]
rs7195915	0.89[ASN][1000 genomes]
rs7195945	0.89[ASN][1000 genomes]
rs7206295	0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7499192	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7501207	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8048583	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8052324	0.85[ASN][1000 genomes]
rs8058882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8060268	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs8062159	0.85[ASN][1000 genomes]
rs9673398	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9673404	0.91[ASN][1000 genomes]
rs9673405	0.92[ASN][1000 genomes]
rs9673519	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9673522	0.92[ASN][1000 genomes]
rs9674009	0.92[ASN][1000 genomes]
rs9888907	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31355600-31365600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31356600-31363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:31358600-31366400	Enhancers	Primary B cells from peripheral blood	blood
5	chr16:31358800-31366000	Enhancers	Primary hematopoietic stem cells	blood
6	chr16:31359000-31365600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr16:31360400-31363600	Weak transcription	Fetal Muscle Leg	muscle
8	chr16:31361200-31368000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr16:31362000-31363600	Weak transcription	Spleen	Spleen
10	chr16:31362800-31363800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr16:31362800-31363800	Flanking Active TSS	GM12878-XiMat	blood
12	chr16:31362800-31364800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr16:31363200-31363600	Enhancers	A549	lung
14	chr16:31363200-31363800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
15	chr16:31363200-31364400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr16:31363200-31364800	Enhancers	Fetal Muscle Trunk	muscle
17	chr16:31363400-31363600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr16:31363400-31363600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:31363400-31363600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr16:31363400-31363600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr16:31363400-31363800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr16:31363400-31363800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr16:31363400-31363800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:31363400-31364200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links