Variant report

Variant	rs856302
Chromosome Location	chr19:38259082-38259083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38256038..38258477-chr19:38258531..38260725,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10407657	0.89[CEU][hapmap]
rs10422056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10424612	0.89[CEU][hapmap]
rs10425671	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11083438	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11083439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11665877	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11667454	0.87[EUR][1000 genomes]
rs11667457	0.87[EUR][1000 genomes]
rs11668384	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11668434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11668558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11670655	0.87[EUR][1000 genomes]
rs11672077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs11883392	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12462485	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12610891	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12972712	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12981237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12982288	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12983298	0.87[EUR][1000 genomes]
rs1643470	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[MKK][hapmap]
rs17306508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17306795	0.90[CHB][hapmap]
rs1871197	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2045909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2126978	0.89[CEU][hapmap]
rs2160640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2385116	0.86[EUR][1000 genomes]
rs241937	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241940	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241942	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241943	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241944	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241946	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241947	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs241951	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs241953	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs241957	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs241959	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs241960	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909106	0.89[EUR][1000 genomes]
rs2927741	0.87[EUR][1000 genomes]
rs2927744	0.89[CEU][hapmap]
rs2972453	0.86[EUR][1000 genomes]
rs2972454	0.84[EUR][1000 genomes]
rs2972456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2972459	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3112435	0.95[EUR][1000 genomes]
rs34351186	0.84[EUR][1000 genomes]
rs34607899	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34782935	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34949193	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35015599	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35214625	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35273320	0.87[EUR][1000 genomes]
rs353406	0.81[AMR][1000 genomes]
rs35415221	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36020184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36092052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3752365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3894129	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4273159	0.81[EUR][1000 genomes]
rs4482404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802066	0.80[EUR][1000 genomes]
rs4802069	0.89[CEU][hapmap]
rs4802134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4803536	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4803566	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57308437	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62108304	0.87[EUR][1000 genomes]
rs62108339	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62108355	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508738	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs6508748	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs697433	1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs7250668	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7253174	0.84[EUR][1000 genomes]
rs7254170	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs7254828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255283	0.89[CEU][hapmap]
rs7255551	0.83[ASN][1000 genomes]
rs8102871	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8103882	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8105694	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8110417	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8111400	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs8113076	0.89[CEU][hapmap]
rs856309	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs856302	RABAC1	cis	cerebellum	SCAN
rs856302	CD3EAP	cis	cerebellum	SCAN
rs856302	ITPKC	cis	cerebellum	SCAN
rs856302	PPP5C	cis	parietal	SCAN
rs856302	ARHGEF1	cis	cerebellum	SCAN
rs856302	CEACAM16	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
2	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
6	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
7	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
9	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
10	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:38246800-38259600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:38246800-38259800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:38247400-38259800	Weak transcription	Placenta	Placenta
14	chr19:38247800-38260000	Weak transcription	Osteobl	bone
15	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
16	chr19:38248400-38264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:38248800-38269400	Weak transcription	NH-A	brain
18	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
19	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:38250400-38259600	Weak transcription	Esophagus	oesophagus
21	chr19:38250600-38262600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr19:38250600-38264000	Strong transcription	Primary T cells from cord blood	blood
23	chr19:38250600-38264400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:38250600-38265000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:38250600-38266400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:38250800-38261400	Strong transcription	Fetal Stomach	stomach
27	chr19:38251000-38259600	Weak transcription	Brain Germinal Matrix	brain
28	chr19:38251400-38261200	Strong transcription	Fetal Muscle Leg	muscle
29	chr19:38251800-38269400	Weak transcription	Gastric	stomach
30	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
31	chr19:38252200-38259600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:38252600-38269000	Weak transcription	NHEK	skin
34	chr19:38253000-38260000	Weak transcription	HepG2	liver
35	chr19:38253400-38259600	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:38253400-38263600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:38253600-38259600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:38253600-38261400	Strong transcription	Fetal Intestine Large	intestine
39	chr19:38253600-38263600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:38253800-38259800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
42	chr19:38254800-38269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:38255400-38262600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:38255400-38264800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:38255600-38259400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:38255600-38261000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:38255600-38263000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:38255600-38264000	Strong transcription	Adipose Nuclei	Adipose
49	chr19:38255600-38264200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:38255800-38259200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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