Variant report

Variant	rs2304232
Chromosome Location	chr19:41762525-41762526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41762234..41765472-chr19:41769358..41771967,3	MCF-7	breast:
2	chr19:41761250..41763518-chr19:41766125..41769056,3	MCF-7	breast:
3	chr19:41754992..41757426-chr19:41761264..41763362,2	MCF-7	breast:
4	chr19:41738381..41740687-chr19:41762333..41764630,2	K562	blood:

Variant related genes	Relation type
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10410836	0.84[EUR][1000 genomes]
rs10421990	0.84[EUR][1000 genomes]
rs1056854	0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs11466345	0.81[JPT][hapmap]
rs11879429	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879435	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879562	0.84[EUR][1000 genomes]
rs11880564	0.85[ASN][1000 genomes]
rs11880729	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881940	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11881953	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12327659	0.84[EUR][1000 genomes]
rs12972266	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12972779	0.87[ASN][1000 genomes]
rs12972949	0.95[ASN][1000 genomes]
rs12974323	0.84[EUR][1000 genomes]
rs12974420	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12976536	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977563	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978323	0.85[CHB][hapmap]
rs12980267	0.82[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12980480	0.84[EUR][1000 genomes]
rs12980942	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12981053	0.87[ASN][1000 genomes]
rs12982872	0.86[ASN][1000 genomes]
rs12983027	0.88[ASN][1000 genomes]
rs12983339	0.93[ASN][1000 genomes]
rs12984160	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12985162	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12985339	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1946612	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1946613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2053086	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241718	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241719	0.85[ASN][1000 genomes]
rs2241720	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2304230	0.84[EUR][1000 genomes]
rs2304231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304235	0.85[ASN][1000 genomes]
rs34322801	0.85[ASN][1000 genomes]
rs34772093	0.94[ASN][1000 genomes]
rs35310790	0.86[ASN][1000 genomes]
rs35501756	0.85[ASN][1000 genomes]
rs35546772	0.95[ASN][1000 genomes]
rs35812313	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745295	0.84[EUR][1000 genomes]
rs3752705	0.84[EUR][1000 genomes]
rs3760659	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3760660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3786556	0.85[ASN][1000 genomes]
rs3816052	0.84[EUR][1000 genomes]
rs4591267	0.90[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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61459202	0.87[ASN][1000 genomes]
rs66724427	0.84[EUR][1000 genomes]
rs67744888	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248164	0.84[EUR][1000 genomes]
rs7250883	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs7256416	0.84[EUR][1000 genomes]
rs7256856	0.84[EUR][1000 genomes]
rs7256873	0.84[ASN][1000 genomes]
rs7257825	0.84[EUR][1000 genomes]
rs7258749	0.84[EUR][1000 genomes]
rs8103839	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105901	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2304232	TSKS	cis	parietal	SCAN
rs2304232	BAX	cis	cerebellum	SCAN
rs2304232	KLC3	cis	parietal	SCAN
rs2304232	PLEKHA4	cis	cerebellum	SCAN
rs2304232	TMEM145	cis	parietal	SCAN

Chromatin state (count:94 , 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	chr19:41737200-41766000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr19:41737400-41766600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:41738800-41767400	Weak transcription	Fetal Brain Male	brain
17	chr19:41739400-41767400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:41739800-41766200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:41742600-41767600	Strong transcription	A549	lung
20	chr19:41745200-41765000	Weak transcription	Fetal Brain Female	brain
21	chr19:41745800-41767200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:41753400-41767000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:41753800-41767400	Strong transcription	NHDF-Ad	bronchial
24	chr19:41754200-41766000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:41754200-41766000	Strong transcription	NHEK	skin
26	chr19:41754200-41767200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:41754600-41767200	Weak transcription	Brain Germinal Matrix	brain
28	chr19:41755000-41767400	Weak transcription	Fetal Thymus	thymus
29	chr19:41755000-41767800	Weak transcription	Hela-S3	cervix
30	chr19:41755000-41768000	Weak transcription	Gastric	stomach
31	chr19:41756200-41764600	Weak transcription	Liver	Liver
32	chr19:41757000-41763400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr19:41757200-41766200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:41757400-41767800	Weak transcription	Right Atrium	heart
35	chr19:41758000-41766000	Strong transcription	Ovary	ovary
36	chr19:41758000-41766000	Strong transcription	HMEC	breast
37	chr19:41758000-41766200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:41758000-41766200	Strong transcription	HSMMtube	muscle
39	chr19:41758000-41767400	Strong transcription	NHLF	lung
40	chr19:41758200-41767400	Strong transcription	NH-A	brain
41	chr19:41758600-41765800	Strong transcription	HUVEC	blood vessel
42	chr19:41758600-41766200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:41758600-41768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:41758800-41766000	Strong transcription	Adipose Nuclei	Adipose
45	chr19:41758800-41766200	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:41759000-41765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:41759200-41766600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:41760000-41767400	Weak transcription	Pancreas	Pancrea
49	chr19:41760200-41767400	Weak transcription	Colonic Mucosa	Colon
50	chr19:41760800-41766000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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