Variant report

Variant	rs10783794
Chromosome Location	chr12:56987179-56987180
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	chr12:56987156..56990068-chr12:56991407..56993523,3	MCF-7	breast:
2	chr12:56986611..56988626-chr12:56993679..56996417,2	K562	blood:

Variant related genes	Relation type
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1020848	0.83[ASN][1000 genomes]
rs10450	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10876913	0.80[ASN][1000 genomes]
rs10876914	0.83[ASN][1000 genomes]
rs10876915	0.83[ASN][1000 genomes]
rs10876916	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1107479	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11171914	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11171916	0.83[ASN][1000 genomes]
rs11171917	0.83[ASN][1000 genomes]
rs11835120	0.83[ASN][1000 genomes]
rs11837319	0.83[ASN][1000 genomes]
rs12229457	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1465081	0.83[ASN][1000 genomes]
rs1563896	0.95[JPT][hapmap]
rs2035081	0.81[CHB][hapmap]
rs2242497	0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2255074	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256341	0.81[ASN][1000 genomes]
rs2290893	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2926740	0.83[ASN][1000 genomes]
rs2950387	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs2950388	0.83[ASN][1000 genomes]
rs2950389	0.85[JPT][hapmap]
rs2950390	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2950393	0.83[ASN][1000 genomes]
rs2950394	0.83[ASN][1000 genomes]
rs2958123	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2958124	0.84[ASN][1000 genomes]
rs2958139	0.83[CHD][hapmap]
rs2958145	0.83[ASN][1000 genomes]
rs2958146	0.83[ASN][1000 genomes]
rs2958153	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2958154	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2958155	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs36012661	0.83[ASN][1000 genomes]
rs4759254	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs67046307	0.83[ASN][1000 genomes]
rs7315472	0.83[ASN][1000 genomes]
rs73337030	0.83[ASN][1000 genomes]
rs7973157	0.83[ASN][1000 genomes]
rs9368	0.86[CEU][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs941207	0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs941209	0.89[JPT][hapmap]
rs9634246	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9634247	0.80[ASN][1000 genomes]
rs9634277	0.80[ASN][1000 genomes]
rs9989034	0.82[ASN][1000 genomes]

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	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv526706	chr12:56961932-56988342	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1043992	chr12:56976326-57010458	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10783794	KRT1	cis	cerebellum	SCAN
rs10783794	OR10A7	cis	parietal	SCAN
rs10783794	PRIM1	cis	cerebellum	SCAN
rs10783794	PRIM1	cis	parietal	SCAN
rs10783794	IL23A	cis	cerebellum	SCAN
rs10783794	HSD17B6	cis	cerebellum	SCAN
rs10783794	RBMS2	cis	multi-tissue	Pritchard
rs10783794	HOXC6	cis	cerebellum	SCAN
rs10783794	ERBB3	cis	parietal	SCAN
rs10783794	LETMD1	cis	cerebellum	SCAN
rs10783794	RAB5B	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56954600-56993400	Weak transcription	Fetal Brain Male	brain
2	chr12:56960000-56987600	Weak transcription	Fetal Heart	heart
3	chr12:56964000-56987800	Weak transcription	Right Atrium	heart
4	chr12:56964200-56992600	Weak transcription	Stomach Mucosa	stomach
5	chr12:56973800-56990600	Weak transcription	Psoas Muscle	Psoas
6	chr12:56975800-56991600	Weak transcription	Small Intestine	intestine
7	chr12:56976000-56990600	Weak transcription	GM12878-XiMat	blood
8	chr12:56976200-56989600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:56976200-56989600	Weak transcription	Colonic Mucosa	Colon
10	chr12:56976200-56991000	Weak transcription	HepG2	liver
11	chr12:56976400-56990800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:56976600-56990800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:56976800-56990200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:56976800-56990800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:56977600-57017000	Strong transcription	Placenta	Placenta
16	chr12:56978200-56990600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:56979600-56989200	Weak transcription	Primary B cells from cord blood	blood
18	chr12:56979600-57020400	Strong transcription	Fetal Stomach	stomach
19	chr12:56979800-56990800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:56981800-56988400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:56982000-56988400	Weak transcription	Brain Germinal Matrix	brain
22	chr12:56982000-56990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:56982200-56987800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:56982400-56989400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:56982400-56990600	Weak transcription	Dnd41	blood
26	chr12:56982600-56987800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:56982600-56988200	Weak transcription	Primary T cells from cord blood	blood
28	chr12:56982600-56989200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:56982600-56989800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:56982800-56987800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:56982800-56987800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:56982800-56987800	Weak transcription	Brain Angular Gyrus	brain
33	chr12:56982800-56987800	Weak transcription	Fetal Kidney	kidney
34	chr12:56982800-56987800	Weak transcription	Right Ventricle	heart
35	chr12:56982800-56988200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:56982800-56988200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:56982800-56989200	Weak transcription	Thymus	Thymus
38	chr12:56982800-56989400	Weak transcription	Pancreas	Pancrea
39	chr12:56982800-56990200	Weak transcription	Gastric	stomach
40	chr12:56982800-56990800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:56982800-56990800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:56982800-56991200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:56983000-56987600	Weak transcription	Liver	Liver
44	chr12:56983000-56987800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:56983000-56987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:56983000-56987800	Weak transcription	Esophagus	oesophagus
47	chr12:56983000-56987800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:56983000-56989400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:56983000-56989400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:56983200-56988800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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