Variant report

Variant	rs6508738
Chromosome Location	chr19:38099700-38099701
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	chr19:38094621..38097474-chr19:38099198..38101401,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1038084	0.84[CEU][hapmap]
rs1038085	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407657	0.84[CEU][hapmap]
rs10417204	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424612	0.84[CEU][hapmap]
rs10425671	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665877	0.84[EUR][1000 genomes]
rs11667454	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11667457	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668434	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]
rs11668558	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs11670655	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672077	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11883392	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1236810	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12972712	0.85[EUR][1000 genomes]
rs12981237	0.84[EUR][1000 genomes]
rs12982288	0.85[EUR][1000 genomes]
rs12983298	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1465434	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17306508	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];0.83[EUR][1000 genomes]
rs17306795	1.00[CHB][hapmap]
rs1871197	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045909	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126978	0.83[CEU][hapmap]
rs2160640	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2199644	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291000	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385116	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385124	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385125	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs241947	0.81[EUR][1000 genomes]
rs241948	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs241951	1.00[CHB][hapmap]
rs2617789	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2927741	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927744	0.84[CEU][hapmap]
rs2972453	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972454	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972456	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972459	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112435	0.85[EUR][1000 genomes]
rs34351186	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34607899	0.87[EUR][1000 genomes]
rs34782935	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35015599	0.85[EUR][1000 genomes]
rs35214625	0.85[EUR][1000 genomes]
rs35273320	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35415221	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36020184	0.84[EUR][1000 genomes]
rs36092052	0.84[EUR][1000 genomes]
rs3752365	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4273159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482404	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs4802066	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802069	0.84[CEU][hapmap]
rs4803216	0.84[CEU][hapmap]
rs4803228	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57308437	0.85[EUR][1000 genomes]
rs62108304	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108339	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62108355	0.83[EUR][1000 genomes]
rs6508729	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7251097	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs7253174	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254828	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs7255283	0.84[CEU][hapmap]
rs8111055	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113076	0.84[CEU][hapmap]
rs856302	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]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6508738	RABAC1	cis	cerebellum	SCAN
rs6508738	ARHGEF1	cis	cerebellum	SCAN
rs6508738	ITPKC	cis	cerebellum	SCAN
rs6508738	CEACAM16	cis	parietal	SCAN
rs6508738	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38086600-38103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:38087200-38100200	Weak transcription	Right Ventricle	heart
3	chr19:38087200-38103000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
5	chr19:38089200-38107200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
6	chr19:38090400-38105200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38090600-38105400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr19:38091200-38101000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38092200-38103400	Weak transcription	Thymus	Thymus
10	chr19:38092400-38102400	Weak transcription	Dnd41	blood
11	chr19:38093400-38100200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:38093600-38102800	Weak transcription	Fetal Brain Female	brain
13	chr19:38093600-38105000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:38093800-38101000	Weak transcription	Psoas Muscle	Psoas
15	chr19:38094600-38102600	Weak transcription	Fetal Brain Male	brain
16	chr19:38094600-38103200	Weak transcription	Brain Germinal Matrix	brain
17	chr19:38095400-38099800	Strong transcription	Left Ventricle	heart
18	chr19:38095400-38107200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr19:38095600-38100000	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:38095600-38100000	ZNF genes & repeats	Colon Smooth Muscle	Colon
21	chr19:38095600-38105000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr19:38095600-38105400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:38095800-38101000	Weak transcription	Fetal Kidney	kidney
24	chr19:38096600-38100400	ZNF genes & repeats	Ovary	ovary
25	chr19:38096800-38099800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr19:38096800-38099800	ZNF genes & repeats	Brain Substantia Nigra	brain
27	chr19:38096800-38105400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
28	chr19:38097000-38099800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr19:38097200-38100000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr19:38097400-38102600	Strong transcription	Brain Angular Gyrus	brain
31	chr19:38097400-38102600	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr19:38097600-38100800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:38098200-38107200	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr19:38098400-38099800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:38098400-38100000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr19:38098400-38100200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
37	chr19:38098600-38100000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:38098800-38099800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
39	chr19:38098800-38100000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:38098800-38100600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38098800-38100600	ZNF genes & repeats	Aorta	Aorta
42	chr19:38099000-38100000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:38099000-38100200	Weak transcription	Gastric	stomach
44	chr19:38099000-38101200	Weak transcription	Colonic Mucosa	Colon
45	chr19:38099400-38100000	ZNF genes & repeats	Fetal Stomach	stomach
46	chr19:38099400-38100000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
47	chr19:38099400-38100800	Weak transcription	Brain Anterior Caudate	brain
48	chr19:38099600-38100000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:38099600-38100400	ZNF genes & repeats	Pancreas	Pancrea
50	chr19:38099600-38101000	Weak transcription	Brain Hippocampus Middle	brain

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