Variant report

Variant	rs2140437
Chromosome Location	chr3:142391847-142391848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11917460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13070239	0.85[ASW][hapmap]
rs13071750	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13074153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078890	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13085261	0.85[ASW][hapmap]
rs13091247	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13095394	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2354858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34392719	0.89[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4594656	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4683427	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278480	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809448	0.84[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7650047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2140437	XRN1	cis	cerebellum	SCAN
rs2140437	TRPC1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
3	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:142382600-142400400	Weak transcription	Gastric	stomach
6	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:142384600-142392400	Weak transcription	HepG2	liver
8	chr3:142384800-142403000	Weak transcription	Liver	Liver
9	chr3:142385800-142415400	Weak transcription	A549	lung
10	chr3:142386400-142411800	Weak transcription	NHEK	skin
11	chr3:142387400-142401800	Weak transcription	Aorta	Aorta
12	chr3:142387400-142404200	Weak transcription	Small Intestine	intestine
13	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
14	chr3:142388200-142393200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:142388200-142393200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:142389200-142392000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:142390000-142392800	Strong transcription	Dnd41	blood
23	chr3:142390000-142406200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:142390400-142393000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:142391000-142392600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:142391200-142394800	Strong transcription	Fetal Intestine Small	intestine
27	chr3:142391200-142395400	Weak transcription	Lung	lung
28	chr3:142391600-142393000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:142391800-142392400	Strong transcription	Fetal Intestine Large	intestine
30	chr3:142391800-142393000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:142391800-142393400	Strong transcription	Primary hematopoietic stem cells	blood

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