Variant report

Variant	rs360094
Chromosome Location	chr1:226064846-226064847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226063406..226070293-chr1:226107715..226112317,7	K562	blood:
2	chr1:225997762..225999546-chr1:226064729..226066981,2	MCF-7	breast:
3	chr1:226061743..226065093-chr1:226081244..226084907,3	MCF-7	breast:
4	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
5	chr1:226058705..226061570-chr1:226062112..226065041,3	K562	blood:
6	chr1:226033230..226036408-chr1:226061975..226066194,3	MCF-7	breast:
7	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143819	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000154380	Chromatin interaction
ENSG00000242861	Chromatin interaction
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs111990	0.86[AFR][1000 genomes]
rs1223244	0.82[EUR][1000 genomes]
rs12747508	0.81[EUR][1000 genomes]
rs168617	0.82[EUR][1000 genomes]
rs168618	0.85[AFR][1000 genomes]
rs168619	0.85[AFR][1000 genomes]
rs2292563	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292564	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2740168	0.85[JPT][hapmap]
rs360060	0.86[EUR][1000 genomes]
rs360076	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs360088	0.83[AFR][1000 genomes]
rs360091	0.87[AFR][1000 genomes]
rs360093	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360095	0.91[AFR][1000 genomes]
rs360096	0.91[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360097	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360098	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs360099	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs360100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360101	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360102	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360103	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs3820236	0.95[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs55936398	0.92[ASN][1000 genomes]
rs6426090	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515156	0.82[EUR][1000 genomes]
rs9919303	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]

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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs360094	PARP1	cis	cerebellum	SCAN
rs360094	TMEM63A	cis	parietal	SCAN
rs360094	TMEM63A	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
3	chr1:226037800-226065200	Weak transcription	Right Atrium	heart
4	chr1:226038800-226065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:226044600-226065800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:226050200-226068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:226051800-226066400	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr1:226054000-226065000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:226054400-226065000	Strong transcription	Lung	lung
10	chr1:226054400-226065600	Strong transcription	Fetal Stomach	stomach
11	chr1:226054400-226065800	Weak transcription	HUVEC	blood vessel
12	chr1:226054600-226065200	Strong transcription	Spleen	Spleen
13	chr1:226054600-226065800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:226054800-226065800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:226055000-226065000	Weak transcription	Psoas Muscle	Psoas
16	chr1:226055000-226065400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:226055000-226065600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:226055000-226066600	Weak transcription	Dnd41	blood
19	chr1:226055200-226065000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:226055200-226065400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:226056200-226065200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:226057200-226065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:226058400-226067200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:226058600-226065600	Strong transcription	K562	blood
25	chr1:226059600-226068800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:226059800-226065000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:226059800-226066600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:226059800-226066800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:226060000-226065000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:226060000-226065200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:226060200-226068600	Weak transcription	NH-A	brain
32	chr1:226060400-226065000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr1:226060600-226066400	Genic enhancers	Placenta	Placenta
34	chr1:226060800-226065000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:226060800-226065400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:226060800-226065600	Genic enhancers	Pancreas	Pancrea
37	chr1:226060800-226066000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:226061000-226065000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:226061000-226065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:226061000-226065200	Strong transcription	Fetal Lung	lung
41	chr1:226061000-226065400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:226061600-226065400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:226062000-226065000	Weak transcription	Osteobl	bone
44	chr1:226062000-226065400	Weak transcription	Fetal Kidney	kidney
45	chr1:226062000-226067200	Genic enhancers	Fetal Intestine Large	intestine
46	chr1:226062200-226065200	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr1:226062200-226065600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:226062200-226065800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:226062400-226065000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:226062400-226065000	Weak transcription	Gastric	stomach

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