Variant report

Variant	rs11928203
Chromosome Location	chr3:142379120-142379121
allele	C/T
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[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13070239	0.85[ASW][hapmap]
rs13071750	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs13074153	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13078890	0.86[AMR][1000 genomes]
rs13085261	0.85[ASW][hapmap]
rs13091247	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13095394	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2140437	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]
rs2354858	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34392719	0.89[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs4594656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683427	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62278480	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6809448	0.84[ASW][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs7650047	0.81[AMR][1000 genomes];0.88[EUR][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
rs11928203	XRN1	cis	cerebellum	SCAN
rs11928203	TRPC1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142369200-142379200	Weak transcription	Dnd41	blood
3	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
4	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:142372000-142382000	Weak transcription	HepG2	liver
6	chr3:142372000-142382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:142372200-142379200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:142372600-142381800	Weak transcription	Fetal Intestine Small	intestine
9	chr3:142372600-142391200	Weak transcription	K562	blood
10	chr3:142376000-142382400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:142376200-142379200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:142376200-142379200	Weak transcription	Liver	Liver
13	chr3:142376200-142379600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:142376200-142382000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:142376400-142379200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:142376400-142381600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:142376600-142388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:142377200-142381600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:142378000-142379400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:142378200-142382200	Weak transcription	Stomach Mucosa	stomach
21	chr3:142378800-142379200	Weak transcription	A549	lung
22	chr3:142379000-142380000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:142379000-142380200	Enhancers	HUES48 Cell Line	embryonic stem cell

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