Variant report

Variant	rs4683427
Chromosome Location	chr3:142409228-142409229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142409223..142411101-chr3:142411877..142413945,2	MCF-7	breast:

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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11928203	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]
rs13071750	0.89[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13074153	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13078890	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13085261	0.81[TSI][hapmap]
rs13091247	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095394	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2140437	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]
rs2354858	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34392719	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs4256152	0.81[TSI][hapmap]
rs4594656	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278480	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809448	0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7650047	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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
rs4683427	XRN1	cis	cerebellum	SCAN
rs4683427	TRPC1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:142385800-142415400	Weak transcription	A549	lung
5	chr3:142386400-142411800	Weak transcription	NHEK	skin
6	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
7	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:142392600-142410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:142392800-142418000	Weak transcription	HepG2	liver
13	chr3:142392800-142425400	Weak transcription	Dnd41	blood
14	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:142393000-142426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:142393400-142426200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:142401200-142410000	Weak transcription	Primary T cells from cord blood	blood
18	chr3:142403000-142412800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr3:142404200-142418000	Weak transcription	HMEC	breast
20	chr3:142404600-142416200	Weak transcription	Fetal Intestine Small	intestine
21	chr3:142405800-142411600	Weak transcription	Fetal Intestine Large	intestine
22	chr3:142407000-142410600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:142407200-142417000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:142408800-142412000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:142408800-142430400	Weak transcription	Liver	Liver

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