Variant report

Variant	rs241937
Chromosome Location	chr19:38310660-38310661
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	chr19:38310273..38312700-chr19:38313306..38315862,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10422056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083438	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665877	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11668384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	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]
rs11668558	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11672077	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12462485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610891	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972712	0.88[AMR][1000 genomes]
rs12981237	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1643470	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1643472	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725490	0.82[EUR][1000 genomes]
rs17306508	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]
rs17306795	0.90[CHB][hapmap]
rs1871197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2160640	0.82[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs241940	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];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241942	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];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241943	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241944	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241946	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241947	0.96[ASN][1000 genomes]
rs241948	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]
rs241953	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs241957	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241959	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241960	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972456	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs34607899	0.88[AMR][1000 genomes]
rs34949193	0.83[AMR][1000 genomes]
rs35015599	0.88[AMR][1000 genomes]
rs35214625	0.88[AMR][1000 genomes]
rs353405	0.81[EUR][1000 genomes]
rs353406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs353409	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353412	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353413	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36020184	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36092052	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3752365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs3894129	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];0.96[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs4802134	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803566	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62108355	0.81[AMR][1000 genomes]
rs6508748	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508752	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs697433	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs7254828	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7255551	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8102871	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8103882	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105694	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110417	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833916	1.00[CHB][hapmap]
rs856302	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]
rs856309	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861308	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs241937	ARHGEF1	cis	cerebellum	SCAN
rs241937	ITPKC	cis	cerebellum	SCAN
rs241937	CD3EAP	cis	cerebellum	SCAN
rs241937	PPP5C	cis	parietal	SCAN
rs241937	CEACAM16	cis	parietal	SCAN
rs241937	TMEM145	cis	parietal	SCAN
rs241937	GSK3A	cis	parietal	SCAN
rs241937	ZNF573	cis	brain	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38308600-38312000	Weak transcription	Aorta	Aorta
2	chr19:38308600-38314800	Weak transcription	Gastric	stomach
3	chr19:38308800-38310800	Weak transcription	Brain Anterior Caudate	brain
4	chr19:38308800-38311600	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:38308800-38311800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:38308800-38312000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:38308800-38312000	Weak transcription	Fetal Intestine Large	intestine
8	chr19:38308800-38312200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr19:38308800-38312200	Weak transcription	Left Ventricle	heart
10	chr19:38308800-38313200	Weak transcription	Esophagus	oesophagus
11	chr19:38308800-38314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:38308800-38314400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:38308800-38314400	Weak transcription	Brain Angular Gyrus	brain
14	chr19:38308800-38314400	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:38308800-38314400	Weak transcription	Right Ventricle	heart
16	chr19:38308800-38314600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38308800-38314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:38308800-38314600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:38309000-38310800	Weak transcription	Fetal Lung	lung
21	chr19:38309000-38311400	Weak transcription	Fetal Kidney	kidney
22	chr19:38309000-38312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:38309000-38313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:38309000-38313200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:38309000-38314200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:38309000-38314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:38309000-38314600	Weak transcription	Fetal Heart	heart
28	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
29	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
30	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
32	chr19:38310000-38312000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:38310000-38312400	Strong transcription	Brain Cingulate Gyrus	brain
34	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:38310200-38311000	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr19:38310200-38311000	Strong transcription	Brain Substantia Nigra	brain
39	chr19:38310200-38311600	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38310200-38312000	Strong transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:38310200-38312000	Strong transcription	Ovary	ovary
42	chr19:38310200-38312600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:38310200-38313800	ZNF genes & repeats	Fetal Brain Male	brain
44	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr19:38310400-38310800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
46	chr19:38310400-38311000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
47	chr19:38310400-38312800	Strong transcription	Brain Hippocampus Middle	brain
48	chr19:38310600-38311200	ZNF genes & repeats	Fetal Stomach	stomach
49	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea

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