Variant report

Variant	rs870238
Chromosome Location	chr3:43070766-43070767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13061038	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095711	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280565	0.89[JPT][hapmap]
rs2936817	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35339908	0.81[ASN][1000 genomes]
rs3732856	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs473467	0.89[JPT][hapmap]
rs476336	0.90[EUR][1000 genomes]
rs477594	0.87[JPT][hapmap]
rs496436	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs504973	0.89[JPT][hapmap]
rs509527	0.90[EUR][1000 genomes]
rs517650	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs536119	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs536572	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs541007	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs56009835	0.90[ASN][1000 genomes]
rs565521	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs590899	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs606336	0.85[ASN][1000 genomes]
rs606724	0.89[EUR][1000 genomes]
rs62247065	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs643663	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs648273	0.90[ASN][1000 genomes]
rs658958	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs660324	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs660446	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs664628	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6806706	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693290	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs697327	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704912	0.92[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs834166	0.81[EUR][1000 genomes]
rs834178	0.85[CEU][hapmap]
rs834188	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs834191	0.89[EUR][1000 genomes]
rs9311333	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882262	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3434201	chr3:43070570-43071102	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs870238	CCR9	cis	parietal	SCAN
rs870238	LYZL4	cis	cerebellum	SCAN
rs870238	C3orf39	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43053600-43073200	Weak transcription	Right Atrium	heart
2	chr3:43059600-43074400	Weak transcription	Lung	lung
3	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
4	chr3:43061000-43072200	Weak transcription	Liver	Liver
5	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:43061800-43073000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:43063000-43077400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:43063400-43072000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:43063600-43072600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:43064000-43077800	Weak transcription	Brain Substantia Nigra	brain
12	chr3:43065200-43072400	Weak transcription	Placenta	Placenta
13	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:43067400-43076200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:43067600-43070800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:43067600-43084000	Weak transcription	Aorta	Aorta
17	chr3:43067800-43071000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:43067800-43071000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:43067800-43074400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:43068000-43070800	Weak transcription	Fetal Thymus	thymus
21	chr3:43068200-43071200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:43068200-43076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:43068800-43070800	Weak transcription	Primary T cells from cord blood	blood
24	chr3:43069600-43071200	Enhancers	Stomach Mucosa	stomach
25	chr3:43069600-43071600	Enhancers	Fetal Intestine Small	intestine
26	chr3:43069800-43071000	Enhancers	Fetal Intestine Large	intestine
27	chr3:43070000-43071200	Enhancers	Gastric	stomach
28	chr3:43070200-43072600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:43070600-43084800	Weak transcription	Esophagus	oesophagus

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