Variant report

Variant	rs947474
Chromosome Location	chr10:6390450-6390451
allele	A/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	chr10:6389914-6390481	GM12878	blood:	n/a	n/a
2	MTA3	chr10:6389399-6390676	GM12878	blood:	n/a	n/a
3	NFIC	chr10:6389401-6390575	GM12878	blood:	n/a	n/a
4	IKZF1	chr10:6389569-6390538	GM12878	blood:	n/a	n/a
5	BCLAF1	chr10:6389901-6390516	GM12878	blood:	n/a	n/a
6	RCOR1	chr10:6389553-6390525	GM12878	blood:	n/a	n/a
7	SPI1	chr10:6389940-6390501	HL-60	blood:	n/a	n/a
8	RUNX3	chr10:6389441-6390591	GM12878	blood:	n/a	n/a
9	EBF1	chr10:6389465-6390479	GM12878	blood:	n/a	n/a
10	RUNX3	chr10:6389439-6390695	GM12878	blood:	n/a	n/a
11	RFX5	chr10:6389965-6390585	GM12878	blood:	n/a	n/a
12	ETS1	chr10:6389932-6390468	GM12878	blood:	n/a	n/a
13	CEBPB	chr10:6389875-6390626	GM12878	blood:	n/a	n/a
14	FOXM1	chr10:6389866-6390547	GM12878	blood:	n/a	n/a
15	ZNF384	chr10:6389522-6390523	GM12878	blood:	n/a	n/a
16	ZNF143	chr10:6390119-6390487	GM12878	blood:	n/a	n/a
17	MAX	chr10:6389944-6390763	NB4	blood:	n/a	n/a
18	RAD21	chr10:6390047-6390456	GM12878	blood:	n/a	n/a
19	STAT5A	chr10:6389576-6390523	GM12878	blood:	n/a	chr10:6390096-6390103 chr10:6389644-6389652
20	MTA3	chr10:6389905-6390466	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:6389833-6390647	GM12878	blood:	n/a	n/a
22	NFATC1	chr10:6389871-6390517	GM12878	blood:	n/a	n/a
23	SP1	chr10:6389908-6390492	GM12878	blood:	n/a	n/a
24	SP1	chr10:6389874-6390519	GM12878	blood:	n/a	chr10:6389890-6389897
25	ATF2	chr10:6389827-6390596	GM12878	blood:	n/a	n/a
26	EP300	chr10:6389516-6390682	GM12878	blood:	n/a	chr10:6389539-6389546 chr10:6390216-6390230
27	PAX5	chr10:6389798-6390617	GM12878	blood:	n/a	n/a
28	POLR2A	chr10:6389951-6390571	GM12891	blood:	n/a	n/a
29	POLR2A	chr10:6389890-6390578	GM12891	blood:	n/a	n/a
30	SPI1	chr10:6390004-6390506	GM12878	blood:	n/a	n/a
31	ATF2	chr10:6389814-6390562	GM12878	blood:	n/a	n/a
32	BCLAF1	chr10:6389894-6390530	GM12878	blood:	n/a	n/a
33	TBL1XR1	chr10:6389557-6390699	GM12878	blood:	n/a	n/a
34	RELA	chr10:6389537-6390595	GM18505	blood:	n/a	n/a
35	FOXM1	chr10:6389420-6390588	GM12878	blood:	n/a	n/a
36	EBF1	chr10:6389499-6390497	GM12878	blood:	n/a	n/a
37	BCL11A	chr10:6389956-6390532	GM12878	blood:	n/a	n/a
38	POU2F2	chr10:6389373-6390601	GM12878	blood:	n/a	chr10:6390162-6390177 chr10:6390164-6390176 chr10:6390162-6390176 chr10:6390165-6390174 chr10:6390165-6390175 chr10:6390165-6390175 chr10:6390166-6390173
39	MAX	chr10:6389798-6390497	GM12878	blood:	n/a	n/a
40	TCF12	chr10:6389947-6390467	GM12878	blood:	n/a	n/a
41	POLR2A	chr10:6389955-6390455	HL-60	blood:	n/a	n/a
42	BATF	chr10:6389932-6390507	GM12878	blood:	n/a	n/a
43	PML	chr10:6389811-6390545	GM12878	blood:	n/a	n/a
44	IRF4	chr10:6389972-6390550	GM12878	blood:	n/a	n/a
45	MXI1	chr10:6389903-6390903	GM12878	blood:	n/a	n/a
46	CUX1	chr10:6389724-6390475	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:6389340-6390621	GM12878	blood:	n/a	n/a
48	RELA	chr10:6389526-6390556	GM10847	blood:	n/a	n/a
49	SMC3	chr10:6389442-6390600	GM12878	blood:	n/a	chr10:6390309-6390317
50	POU2F2	chr10:6389687-6390476	GM12891	blood:	n/a	chr10:6390162-6390177 chr10:6390164-6390176 chr10:6390162-6390176 chr10:6390165-6390174 chr10:6390165-6390175 chr10:6390165-6390175 chr10:6390166-6390173

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6388010..6391003-chr10:6392017..6395362,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212743	TF binding region
ENSG00000212743	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10752291	0.86[EUR][1000 genomes]
rs10796035	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10796038	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10796040	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10796045	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11258213	0.82[CHD][hapmap]
rs11258264	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570527	0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2146900	0.83[EUR][1000 genomes]
rs2181623	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2387397	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4558075	0.86[EUR][1000 genomes]
rs4589176	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4750316	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7090696	0.81[EUR][1000 genomes]
rs7917676	0.84[CHB][hapmap]
rs947471	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv5676	chr10:6381200-6428950	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Rheumatoid arthritis	24390342	GWAS catalog
Type 1 diabetes	18978792	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs947474	RRAD	trans	brain	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6357200-6397400	Weak transcription	Pancreas	Pancrea
2	chr10:6388200-6391200	Flanking Active TSS	Dnd41	blood
3	chr10:6388600-6390600	Enhancers	A549	lung
4	chr10:6388600-6390600	Enhancers	HSMMtube	muscle
5	chr10:6388600-6390800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr10:6388800-6390600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:6388800-6390800	Enhancers	Fetal Thymus	thymus
8	chr10:6388800-6391600	Enhancers	Fetal Brain Male	brain
9	chr10:6389000-6390600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:6389000-6391200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr10:6389000-6392600	Enhancers	Primary hematopoietic stem cells	blood
12	chr10:6389200-6390600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr10:6389200-6390600	Enhancers	Brain Angular Gyrus	brain
14	chr10:6389200-6390600	Enhancers	Brain Cingulate Gyrus	brain
15	chr10:6389200-6390600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr10:6389200-6390800	Enhancers	Brain Substantia Nigra	brain
17	chr10:6389200-6391200	Enhancers	Fetal Brain Female	brain
18	chr10:6389400-6390600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr10:6389400-6390600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:6389400-6390600	Enhancers	Adipose Nuclei	Adipose
21	chr10:6389400-6390600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:6389400-6390600	Enhancers	Fetal Stomach	stomach
23	chr10:6389400-6390600	Flanking Active TSS	Thymus	Thymus
24	chr10:6389400-6391200	Flanking Active TSS	GM12878-XiMat	blood
25	chr10:6389600-6390600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr10:6389600-6390600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr10:6389600-6390600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:6389600-6390600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr10:6389600-6390800	Enhancers	Brain Germinal Matrix	brain
30	chr10:6389600-6390800	Enhancers	Fetal Lung	lung
31	chr10:6389600-6391000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr10:6389600-6391200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:6389800-6390600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr10:6389800-6390600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:6389800-6390600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr10:6389800-6391000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:6390000-6390600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr10:6390000-6390800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:6390000-6390800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:6390000-6391000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr10:6390000-6391000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr10:6390000-6391000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr10:6390000-6391200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr10:6390000-6392000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr10:6390000-6392200	Weak transcription	Psoas Muscle	Psoas
46	chr10:6390000-6393600	Weak transcription	Lung	lung
47	chr10:6390200-6390600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr10:6390200-6390600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:6390200-6390600	Enhancers	Stomach Smooth Muscle	stomach
50	chr10:6390200-6391400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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