Variant report

Variant	rs241948
Chromosome Location	chr19:38265652-38265653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10407657	0.89[CEU][hapmap]
rs10422056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10425671	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11083439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11668434	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]
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]
rs11672077	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs11883392	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1643470	1.00[CHB][hapmap]
rs17306508	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]
rs17306795	0.90[CHB][hapmap]
rs1871197	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2126978	0.89[CEU][hapmap]
rs2160640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs241937	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs241940	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs241941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs241942	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs241951	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs2927744	0.89[CEU][hapmap]
rs2972456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3752365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3894129	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4482404	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]
rs4802069	0.89[CEU][hapmap]
rs4802134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6508738	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs697433	1.00[CHB][hapmap]
rs7250331	1.00[YRI][hapmap]
rs7254170	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs7254828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7255283	0.89[CEU][hapmap]
rs8111400	1.00[CHB][hapmap]
rs8113076	0.89[CEU][hapmap]
rs856302	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]

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
rs241948	CEACAM16	cis	parietal	SCAN
rs241948	ITPKC	cis	cerebellum	SCAN
rs241948	PPP5C	cis	parietal	SCAN
rs241948	RABAC1	cis	cerebellum	SCAN
rs241948	ARHGEF1	cis	cerebellum	SCAN
rs241948	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
2	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
3	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
4	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
5	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
7	chr19:38248800-38269400	Weak transcription	NH-A	brain
8	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
9	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:38250600-38266400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:38251800-38269400	Weak transcription	Gastric	stomach
12	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
13	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:38252600-38269000	Weak transcription	NHEK	skin
15	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
16	chr19:38254800-38269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:38255800-38266400	ZNF genes & repeats	Liver	Liver
18	chr19:38256800-38269400	Weak transcription	NHLF	lung
19	chr19:38258400-38267600	Weak transcription	K562	blood
20	chr19:38258800-38269200	Weak transcription	HSMMtube	muscle
21	chr19:38259200-38269200	Weak transcription	Brain Angular Gyrus	brain
22	chr19:38259200-38269200	Weak transcription	Fetal Kidney	kidney
23	chr19:38259200-38269200	Weak transcription	HSMM	muscle
24	chr19:38259200-38269400	Weak transcription	Psoas Muscle	Psoas
25	chr19:38259400-38269200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:38260200-38269000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:38260200-38269200	Weak transcription	Fetal Thymus	thymus
28	chr19:38260800-38269000	Weak transcription	Thymus	Thymus
29	chr19:38260800-38269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:38260800-38269200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:38260800-38269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:38260800-38269400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:38261000-38269000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:38261000-38269200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:38261000-38269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:38261000-38269200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:38261000-38269200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr19:38261200-38269000	Weak transcription	Pancreas	Pancrea
39	chr19:38261200-38269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:38261200-38269200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:38261200-38269200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:38261200-38269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38261200-38269200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:38261200-38269200	Weak transcription	HepG2	liver
45	chr19:38261200-38269200	Weak transcription	Osteobl	bone
46	chr19:38261200-38269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:38261200-38269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:38261200-38269400	Weak transcription	Esophagus	oesophagus
49	chr19:38261200-38269400	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:38261200-38269400	Weak transcription	Placenta	Placenta

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