Variant report

Variant	rs730050
Chromosome Location	chr3:52348364-52348365
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr3:52347293-52348568	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52347073-52348785	GM12878	blood:	n/a	n/a
3	RELA	chr3:52347222-52348414	GM18951	blood:	n/a	n/a
4	RUNX3	chr3:52347312-52348624	GM12878	blood:	n/a	n/a
5	STAT5A	chr3:52347585-52348410	GM12878	blood:	n/a	n/a
6	FOS	chr3:52347669-52348830	HUVEC	blood vessel:	n/a	chr3:52348693-52348703 chr3:52348693-52348703 chr3:52348692-52348704 chr3:52347940-52347951 chr3:52348694-52348703 chr3:52348693-52348702 chr3:52348695-52348702
7	RCOR1	chr3:52347252-52348562	GM12878	blood:	n/a	n/a
8	ATF2	chr3:52347421-52348376	GM12878	blood:	n/a	n/a
9	TCF12	chr3:52347581-52348407	SK-N-SH	brain:	n/a	chr3:52347793-52347801
10	RXRA	chr3:52347547-52348371	SK-N-SH	brain:	n/a	chr3:52347994-52348014 chr3:52347997-52348010 chr3:52347996-52348010
11	NFIC	chr3:52347224-52348841	GM12878	blood:	n/a	n/a
12	JUND	chr3:52347489-52348392	SK-N-SH	brain:	n/a	chr3:52347940-52347951
13	SPI1	chr3:52347026-52348421	GM12878	blood:	n/a	n/a
14	MTA3	chr3:52346992-52348955	GM12878	blood:	n/a	n/a
15	BCLAF1	chr3:52347625-52348461	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52347614..52350493-chr3:52351552..52354517,2	K562	blood:
2	chr3:52347090..52349395-chr3:52447262..52449654,2	K562	blood:
3	chr3:52336392..52338122-chr3:52347740..52349816,2	K562	blood:
4	chr3:52311115..52314104-chr3:52347391..52350220,2	K562	blood:
5	chr3:52272103..52274162-chr3:52347959..52349801,2	MCF-7	breast:

Variant related genes	Relation type
DNAH1	TF binding region
ENSG00000243224	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1060330	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs11717383	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs13094687	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs164640	0.82[JPT][hapmap]
rs181274	0.81[JPT][hapmap]
rs187084	0.82[JPT][hapmap]
rs2272088	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2276834	0.95[ASN][1000 genomes]
rs34228726	0.81[ASN][1000 genomes]
rs34569561	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs352139	0.82[JPT][hapmap]
rs352140	0.82[JPT][hapmap]
rs352158	0.81[CHB][hapmap]
rs352162	0.82[JPT][hapmap]
rs352163	0.82[JPT][hapmap]
rs352165	0.82[JPT][hapmap]
rs352166	0.82[JPT][hapmap]
rs352167	0.82[JPT][hapmap]
rs352168	0.82[JPT][hapmap]
rs352169	0.82[JPT][hapmap]
rs352170	0.82[JPT][hapmap]
rs353547	0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3844291	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs3852063	0.88[ASN][1000 genomes]
rs3852064	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs57615517	0.80[ASN][1000 genomes]
rs59565798	0.81[ASN][1000 genomes]
rs610060	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap]
rs6445358	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs648514	0.87[MEX][hapmap]
rs7614727	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs7618915	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs7622851	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7629072	0.93[ASN][1000 genomes]
rs9311474	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
4	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
7	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
8	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs730050	FLJ12442	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
2	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
8	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:52334200-52349600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:52338400-52351400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:52339800-52351200	Weak transcription	Right Ventricle	heart
13	chr3:52342600-52351200	Weak transcription	Fetal Lung	lung
14	chr3:52342600-52351200	Weak transcription	Pancreas	Pancrea
15	chr3:52343000-52351200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:52343200-52351200	Weak transcription	Gastric	stomach
17	chr3:52343800-52350800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52344200-52348600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:52344400-52351200	Weak transcription	Ovary	ovary
20	chr3:52344600-52351200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:52344800-52349600	Weak transcription	Liver	Liver
23	chr3:52344800-52351200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:52344800-52351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:52345200-52351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:52345200-52351200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:52345400-52348600	Weak transcription	Fetal Thymus	thymus
28	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:52345600-52351200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:52345800-52348400	Weak transcription	Fetal Stomach	stomach
32	chr3:52345800-52348600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:52345800-52349000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:52345800-52351200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:52345800-52351200	Weak transcription	Fetal Intestine Large	intestine
36	chr3:52345800-52351600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:52345800-52351600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:52346000-52349400	Weak transcription	Fetal Brain Female	brain
39	chr3:52346200-52349400	Weak transcription	Brain Germinal Matrix	brain
40	chr3:52346200-52349400	Weak transcription	Fetal Brain Male	brain
41	chr3:52346200-52349600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:52346200-52349800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:52346200-52351200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:52346400-52351400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:52346400-52351400	Weak transcription	Primary T cells from cord blood	blood
46	chr3:52346600-52349400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:52346800-52349200	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:52346800-52349400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:52347000-52348600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:52347000-52348600	Enhancers	Fetal Muscle Trunk	muscle

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