Variant report

Variant	rs9660924
Chromosome Location	chr1:226371939-226371940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226370401..226372678-chr1:226386558..226389144,3	K562	blood:
2	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
3	chr1:226343198..226345651-chr1:226370784..226374218,4	K562	blood:
4	chr1:226338462..226340650-chr1:226371216..226373411,2	K562	blood:
5	chr1:226251126..226252830-chr1:226370586..226372718,2	K562	blood:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000270598	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10732276	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799337	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799340	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915952	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915954	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12032630	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047894	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12136759	0.91[MEX][hapmap]
rs1877155	0.83[MEX][hapmap]
rs2306121	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2889539	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008192	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3914142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653718	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653722	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9286997	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9286998	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9659225	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9659397	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9660696	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9660874	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9661836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662709	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9725308	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9725342	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9728014	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9728310	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9729232	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9729554	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9660924	PARP1	cis	cerebellum	SCAN
rs9660924	ACBD3	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:226349000-226373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:226350000-226373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:226352200-226372800	Weak transcription	Fetal Kidney	kidney
5	chr1:226352600-226372200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:226352600-226372400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:226352600-226372800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:226352600-226373000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:226352600-226373400	Weak transcription	Esophagus	oesophagus
10	chr1:226352800-226372000	Weak transcription	Colonic Mucosa	Colon
11	chr1:226353000-226372000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:226353200-226372000	Weak transcription	HUVEC	blood vessel
13	chr1:226353400-226372400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:226353600-226372000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:226353800-226372800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:226354000-226372400	Weak transcription	Thymus	Thymus
17	chr1:226354200-226373000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:226358800-226373400	Weak transcription	Gastric	stomach
19	chr1:226360800-226372000	Weak transcription	Primary T cells from cord blood	blood
20	chr1:226361000-226372800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:226364000-226372000	Weak transcription	Aorta	Aorta
22	chr1:226364000-226373800	Weak transcription	Spleen	Spleen
23	chr1:226367800-226372000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:226368200-226373000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:226368600-226372800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:226368800-226372800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:226369200-226372600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:226369200-226372800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:226369400-226372000	Weak transcription	Brain Substantia Nigra	brain
30	chr1:226369400-226372200	Genic enhancers	Osteobl	bone
31	chr1:226369600-226372000	Enhancers	Placenta	Placenta
32	chr1:226369600-226372000	Enhancers	Small Intestine	intestine
33	chr1:226369600-226373400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:226369800-226372800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:226369800-226373200	Enhancers	Primary B cells from peripheral blood	blood
36	chr1:226370000-226372400	Strong transcription	Fetal Lung	lung
37	chr1:226370200-226372800	Weak transcription	Fetal Brain Male	brain
38	chr1:226370200-226373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:226370400-226372000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:226370400-226372000	Weak transcription	Ovary	ovary
41	chr1:226370400-226372200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:226370400-226372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:226370400-226372400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:226370400-226372400	Strong transcription	Fetal Stomach	stomach
45	chr1:226370400-226372800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:226370400-226373000	Weak transcription	Pancreas	Pancrea
47	chr1:226370400-226373000	Weak transcription	Right Ventricle	heart
48	chr1:226370400-226373200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:226370600-226372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:226370600-226372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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