Variant report

Variant	rs7250883
Chromosome Location	chr19:41760033-41760034
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	chr19:41759028..41761075-chr19:41768130..41769668,2	MCF-7	breast:
2	chr19:41759149..41762027-chr19:41770272..41772414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056854	0.82[JPT][hapmap]
rs11879429	0.97[ASN][1000 genomes]
rs11879435	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs11880564	0.82[ASN][1000 genomes]
rs11880729	0.97[ASN][1000 genomes]
rs11881940	0.94[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11881953	0.86[ASN][1000 genomes]
rs11882467	0.89[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12972266	0.86[ASN][1000 genomes]
rs12972779	0.85[ASN][1000 genomes]
rs12972949	0.92[ASN][1000 genomes]
rs12974420	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12976536	0.86[ASN][1000 genomes]
rs12977563	0.97[ASN][1000 genomes]
rs12978323	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs12980267	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];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980942	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12981053	0.85[ASN][1000 genomes]
rs12982872	0.84[ASN][1000 genomes]
rs12983027	0.85[ASN][1000 genomes]
rs12983339	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12984160	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12985162	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12985339	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1946612	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1946613	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2053086	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2241718	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241719	0.82[ASN][1000 genomes]
rs2241720	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2304231	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2304232	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2304235	0.83[ASN][1000 genomes]
rs34322801	0.82[ASN][1000 genomes]
rs34772093	0.91[ASN][1000 genomes]
rs35310790	0.84[ASN][1000 genomes]
rs35501756	0.82[ASN][1000 genomes]
rs35546772	0.92[ASN][1000 genomes]
rs35812313	0.92[ASN][1000 genomes]
rs3760659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760660	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3786556	0.83[ASN][1000 genomes]
rs4591267	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4802112	0.89[CEU][hapmap]
rs4802115	0.81[EUR][1000 genomes]
rs4803451	0.80[EUR][1000 genomes]
rs61459202	0.85[ASN][1000 genomes]
rs67744888	0.92[ASN][1000 genomes]
rs7256873	0.82[ASN][1000 genomes]
rs8103839	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs8105901	0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7250883	SLC6A16	cis	cerebellum	SCAN
rs7250883	FOSB	cis	parietal	SCAN
rs7250883	SLC1A5	cis	cerebellum	SCAN
rs7250883	SLC1A5	cis	parietal	SCAN
rs7250883	PSG8	cis	parietal	SCAN
rs7250883	BAX	cis	cerebellum	SCAN
rs7250883	PSG2	cis	parietal	SCAN
rs7250883	KCNJ14	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
3	chr19:41733200-41767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:41733200-41767200	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr19:41736000-41767200	Strong transcription	Osteobl	bone
6	chr19:41736000-41767400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:41736400-41767800	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr19:41736600-41766200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:41736600-41766600	Strong transcription	Fetal Stomach	stomach
10	chr19:41736600-41767000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:41736600-41767200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:41736600-41767400	Strong transcription	HSMM	muscle
13	chr19:41736600-41767800	Weak transcription	Brain Angular Gyrus	brain
14	chr19:41736800-41762400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:41737200-41766000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:41737400-41766600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:41738000-41761000	Strong transcription	Colon Smooth Muscle	Colon
18	chr19:41738800-41767400	Weak transcription	Fetal Brain Male	brain
19	chr19:41739400-41767400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:41739800-41766200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:41742600-41767600	Strong transcription	A549	lung
22	chr19:41743800-41761200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:41745200-41765000	Weak transcription	Fetal Brain Female	brain
24	chr19:41745600-41760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:41745800-41762200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:41745800-41767200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:41753400-41767000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:41753800-41767400	Strong transcription	NHDF-Ad	bronchial
29	chr19:41754200-41766000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:41754200-41766000	Strong transcription	NHEK	skin
31	chr19:41754200-41767200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:41754600-41767200	Weak transcription	Brain Germinal Matrix	brain
33	chr19:41754800-41760200	Strong transcription	Fetal Intestine Small	intestine
34	chr19:41755000-41762400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:41755000-41767400	Weak transcription	Fetal Thymus	thymus
36	chr19:41755000-41767800	Weak transcription	Hela-S3	cervix
37	chr19:41755000-41768000	Weak transcription	Gastric	stomach
38	chr19:41756000-41760200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:41756200-41764600	Weak transcription	Liver	Liver
40	chr19:41756400-41762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:41756400-41762400	Weak transcription	Fetal Kidney	kidney
42	chr19:41756800-41762200	Weak transcription	Brain Substantia Nigra	brain
43	chr19:41757000-41762200	Weak transcription	Brain Anterior Caudate	brain
44	chr19:41757000-41763400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:41757200-41766200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:41757400-41767800	Weak transcription	Right Atrium	heart
47	chr19:41758000-41760400	Strong transcription	Aorta	Aorta
48	chr19:41758000-41760600	Strong transcription	Fetal Lung	lung
49	chr19:41758000-41760800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:41758000-41766000	Strong transcription	Ovary	ovary

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