Variant report

Variant	rs7540065
Chromosome Location	chr1:173449036-173449037
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	POLR2A	chr1:173448739-173449085	K562	blood:	n/a	n/a
2	ATF1	chr1:173448917-173449124	K562	blood:	n/a	n/a
3	SPI1	chr1:173448859-173449061	K562	blood:	n/a	n/a
4	BACH1	chr1:173448818-173449171	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:173448564-173449172	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:173448718-173449054	H1-hESC	embryonic stem cell:	n/a	n/a
7	BACH1	chr1:173448851-173449171	K562	blood:	n/a	n/a
8	MAFK	chr1:173448826-173449189	IMR90	lung:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
9	MAFK	chr1:173448837-173449174	HepG2	liver:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
10	MYC	chr1:173448760-173449134	K562	blood:	n/a	n/a
11	MAFF	chr1:173448843-173449168	HepG2	liver:	n/a	chr1:173449001-173449019
12	MAFK	chr1:173448776-173449189	H1-hESC	embryonic stem cell:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
13	POLR2A	chr1:173448804-173449072	MCF10A-Er-Src	breast:	n/a	n/a
14	MAFK	chr1:173448828-173449188	Hela-S3	cervix:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
15	IRF1	chr1:173448222-173449297	K562	blood:	n/a	chr1:173448270-173448281 chr1:173448945-173448959 chr1:173448943-173448957 chr1:173448462-173448471 chr1:173448947-173448957 chr1:173448946-173448958
16	MAX	chr1:173448727-173449066	K562	blood:	n/a	n/a
17	IRF1	chr1:173448562-173449173	K562	blood:	n/a	chr1:173448945-173448959 chr1:173448943-173448957 chr1:173448947-173448957 chr1:173448946-173448958
18	MAFF	chr1:173448701-173449406	K562	blood:	n/a	chr1:173449001-173449019
19	MYC	chr1:173448732-173449170	K562	blood:	n/a	n/a
20	MAFK	chr1:173448669-173449238	K562	blood:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
21	EP300	chr1:173448627-173449117	K562	blood:	n/a	n/a
22	MAFK	chr1:173448825-173449168	HepG2	liver:	n/a	chr1:173449004-173449013 chr1:173449002-173449017
23	POLR2A	chr1:173446081-173449810	K562	blood:	n/a	n/a
24	MYC	chr1:173448783-173449126	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173447936..173449773-chr1:173832296..173834859,2	K562	blood:
2	chr1:173442552..173449186-chr1:173835087..173838637,8	MCF-7	breast:
3	chr1:173446841..173450176-chr1:173473892..173477707,4	K562	blood:
4	chr1:173447238..173449255-chr1:173683141..173684861,2	K562	blood:
5	chr1:173448175..173449804-chr1:173683297..173685231,2	MCF-7	breast:
6	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
7	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:

Variant related genes	Relation type
PRDX6	TF binding region
ENSG00000117593	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10737301	0.84[CEU][hapmap]
rs10753078	0.84[CEU][hapmap]
rs10753081	0.95[ASN][1000 genomes]
rs10753082	0.83[AFR][1000 genomes]
rs10753083	0.86[YRI][hapmap]
rs10798282	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10912617	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10912618	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs10912656	0.87[CHB][hapmap]
rs12065426	0.83[MEX][hapmap]
rs12075314	0.86[AFR][1000 genomes]
rs12077271	0.88[AFR][1000 genomes]
rs12080722	0.82[AFR][1000 genomes]
rs12092383	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs12140760	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12565753	0.84[AFR][1000 genomes]
rs12744504	0.84[CEU][hapmap]
rs12745058	0.90[AFR][1000 genomes]
rs1359460	0.85[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1461022	0.80[AFR][1000 genomes]
rs1547154	0.85[AFR][1000 genomes]
rs1886638	0.86[YRI][hapmap]
rs3934575	0.84[CEU][hapmap]
rs3934576	0.84[CEU][hapmap]
rs4244195	0.84[CEU][hapmap]
rs4255417	0.89[ASN][1000 genomes]
rs4276950	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs4294450	0.84[CEU][hapmap]
rs4310474	0.84[CEU][hapmap]
rs4325171	0.87[ASN][1000 genomes]
rs4382766	0.93[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4539167	0.84[CEU][hapmap]
rs4573551	0.81[AFR][1000 genomes]
rs4611	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916220	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4916355	0.84[ASN][1000 genomes]
rs4916358	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4916359	0.94[ASN][1000 genomes]
rs4916361	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4916362	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4916363	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4916366	0.86[AFR][1000 genomes]
rs4916367	0.86[AFR][1000 genomes]
rs55654074	0.87[ASN][1000 genomes]
rs6425231	0.81[ASN][1000 genomes]
rs6425233	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs6696012	0.93[ASN][1000 genomes]
rs6699094	0.82[CEU][hapmap]
rs6702835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516544	0.86[AFR][1000 genomes]
rs7530469	0.84[CEU][hapmap]
rs7535963	0.86[AFR][1000 genomes]
rs7537938	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.87[ASN][1000 genomes]
rs7549074	0.84[CEU][hapmap]
rs7551305	0.84[AFR][1000 genomes]
rs7556003	0.81[ASN][1000 genomes]
rs912767	0.83[MEX][hapmap]
rs912768	0.88[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9425718	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9425719	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9425723	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425724	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7540065	GPR52	cis	parietal	SCAN
rs7540065	TNFSF18	cis	cerebellum	SCAN
rs7540065	TNFSF4	cis	parietal	SCAN
rs7540065	SLC9A11	cis	parietal	SCAN
rs7540065	PRDX6	cis	cerebellum	SCAN
rs7540065	ANKRD36BP1	cis	cerebellum	SCAN
rs7540065	DARS2	cis	parietal	SCAN
rs7540065	PRDX6	cis	parietal	SCAN
rs7540065	DARS2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173446600-173449600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:173446800-173449600	Active TSS	Right Atrium	heart
3	chr1:173447400-173449400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:173447400-173449600	Transcr. at gene 5' and 3'	K562	blood
5	chr1:173447600-173449200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:173447600-173449400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:173447600-173449600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:173447600-173449600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:173447600-173449600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:173447600-173449600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:173447600-173450400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:173447600-173450400	Weak transcription	Aorta	Aorta
13	chr1:173447600-173450400	Weak transcription	Gastric	stomach
14	chr1:173447600-173450400	Weak transcription	Spleen	Spleen
15	chr1:173447800-173449200	Active TSS	Brain Anterior Caudate	brain
16	chr1:173447800-173449400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:173447800-173449400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:173447800-173449600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
19	chr1:173447800-173449600	Active TSS	Right Ventricle	heart
20	chr1:173447800-173449800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:173447800-173450200	Weak transcription	Brain Germinal Matrix	brain
22	chr1:173447800-173450400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:173447800-173450400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:173447800-173450400	Weak transcription	Esophagus	oesophagus
25	chr1:173447800-173452800	Weak transcription	Pancreas	Pancrea
26	chr1:173448000-173449200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:173448000-173449200	Active TSS	Brain Hippocampus Middle	brain
28	chr1:173448000-173449400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:173448000-173449400	Enhancers	Fetal Heart	heart
30	chr1:173448000-173449400	Enhancers	Fetal Lung	lung
31	chr1:173448000-173449600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:173448000-173449600	Enhancers	Colon Smooth Muscle	Colon
33	chr1:173448000-173449800	Weak transcription	Fetal Thymus	thymus
34	chr1:173448000-173450000	Weak transcription	Fetal Brain Female	brain
35	chr1:173448000-173450200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:173448000-173450200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:173448000-173450400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:173448000-173450400	Weak transcription	Left Ventricle	heart
39	chr1:173448000-173450400	Weak transcription	Lung	lung
40	chr1:173448000-173450600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:173448000-173451400	Weak transcription	Colonic Mucosa	Colon
42	chr1:173448000-173477000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:173448200-173449200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
44	chr1:173448200-173449200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:173448200-173449200	Active TSS	Placenta	Placenta
46	chr1:173448200-173449400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr1:173448200-173449400	Enhancers	Brain Angular Gyrus	brain
48	chr1:173448200-173449400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:173448200-173449600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
50	chr1:173448200-173450000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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