Variant report

Variant	rs11668434
Chromosome Location	chr19:38207632-38207633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38207479..38209787-chr19:38374295..38376201,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038084	0.89[CEU][hapmap]
rs1038085	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10407657	0.89[CEU][hapmap]
rs10417204	0.83[EUR][1000 genomes]
rs10422056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs10424612	0.89[CEU][hapmap]
rs10425671	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11083438	0.88[AMR][1000 genomes]
rs11083439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs11665877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11667454	0.93[EUR][1000 genomes]
rs11667457	0.93[EUR][1000 genomes]
rs11668384	0.84[AMR][1000 genomes]
rs11668558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670655	0.93[EUR][1000 genomes]
rs11672077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs11883392	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12462485	0.88[AMR][1000 genomes]
rs12610891	0.84[AMR][1000 genomes]
rs12972712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981237	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12982288	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983298	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17306508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306795	0.90[CHB][hapmap]
rs1871197	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2045909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2126978	0.89[CEU][hapmap]
rs2160640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2199644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2291000	0.86[EUR][1000 genomes]
rs2385116	0.92[EUR][1000 genomes]
rs2385124	0.83[EUR][1000 genomes]
rs2385125	0.81[EUR][1000 genomes]
rs241937	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs241940	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs241941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs241942	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs241943	0.92[AMR][1000 genomes]
rs241944	0.92[AMR][1000 genomes]
rs241946	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs241947	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs241948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs241951	0.90[CHB][hapmap]
rs241953	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs241957	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs241959	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs241960	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2909106	0.92[EUR][1000 genomes]
rs2927741	0.93[EUR][1000 genomes]
rs2927744	0.89[CEU][hapmap]
rs2972453	0.92[EUR][1000 genomes]
rs2972454	0.91[EUR][1000 genomes]
rs2972456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2972459	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3112435	0.98[EUR][1000 genomes]
rs34351186	0.90[EUR][1000 genomes]
rs34607899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34782935	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34949193	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35015599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35214625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35273320	0.93[EUR][1000 genomes]
rs353406	0.81[AMR][1000 genomes]
rs35415221	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36020184	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36092052	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3752365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894129	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs4273159	0.87[EUR][1000 genomes]
rs4482404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802066	0.87[EUR][1000 genomes]
rs4802069	0.89[CEU][hapmap]
rs4802134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs4803216	0.89[CEU][hapmap]
rs4803228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4803536	0.84[AMR][1000 genomes]
rs4803566	0.84[AMR][1000 genomes]
rs57308437	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108304	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62108339	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62108355	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508738	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs6508748	0.84[AMR][1000 genomes]
rs697433	0.84[AMR][1000 genomes]
rs7250668	0.84[AMR][1000 genomes]
rs7251097	1.00[JPT][hapmap]
rs7253174	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7254170	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7254828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7255283	0.89[CEU][hapmap]
rs8102871	0.84[AMR][1000 genomes]
rs8103882	0.84[AMR][1000 genomes]
rs8105694	0.84[AMR][1000 genomes]
rs8110417	0.84[AMR][1000 genomes]
rs8113076	0.89[CEU][hapmap]
rs856302	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]
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
rs11668434	CD3EAP	cis	cerebellum	SCAN
rs11668434	RABAC1	cis	cerebellum	SCAN
rs11668434	ARHGEF1	cis	cerebellum	SCAN
rs11668434	PPP5C	cis	parietal	SCAN
rs11668434	CEACAM16	cis	parietal	SCAN
rs11668434	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184400-38208800	Weak transcription	HepG2	liver
3	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
9	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
10	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
11	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
12	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
13	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
16	chr19:38197600-38208800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:38198800-38208800	Weak transcription	Fetal Brain Male	brain
18	chr19:38198800-38209000	Weak transcription	Spleen	Spleen
19	chr19:38198800-38209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:38198800-38209200	Weak transcription	Gastric	stomach
21	chr19:38198800-38209400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:38198800-38209800	Weak transcription	Esophagus	oesophagus
23	chr19:38199000-38209000	Weak transcription	Fetal Kidney	kidney
24	chr19:38199000-38209000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:38199000-38209200	Weak transcription	Pancreas	Pancrea
26	chr19:38199000-38209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:38199000-38209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:38199000-38209400	Weak transcription	HSMM	muscle
29	chr19:38199600-38209000	Weak transcription	Small Intestine	intestine
30	chr19:38200400-38209000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:38200400-38209000	Weak transcription	Brain Anterior Caudate	brain
32	chr19:38200400-38209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:38200400-38209200	Weak transcription	NHDF-Ad	bronchial
34	chr19:38200400-38209400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:38200600-38209400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:38200800-38208800	Weak transcription	Fetal Brain Female	brain
37	chr19:38200800-38209000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:38200800-38209200	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:38200800-38209200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:38201200-38209200	Weak transcription	Thymus	Thymus
41	chr19:38201400-38208800	Weak transcription	Brain Germinal Matrix	brain
42	chr19:38201400-38209200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:38202000-38209200	Weak transcription	Colonic Mucosa	Colon
44	chr19:38202400-38209000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:38202400-38209200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:38202400-38209200	Weak transcription	Osteobl	bone
47	chr19:38202600-38209000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:38202600-38209000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:38202600-38209000	Weak transcription	Fetal Intestine Large	intestine
50	chr19:38202600-38209000	Weak transcription	Right Ventricle	heart

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