Variant report

Variant	rs9286998
Chromosome Location	chr1:226360795-226360796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226358815..226361446-chr1:226363128..226365124,4	K562	blood:
2	chr1:226349407..226351925-chr1:226359962..226362068,2	MCF-7	breast:
3	chr1:226358815..226361427-chr1:226363128..226364721,2	K562	blood:
4	chr1:226356179..226357804-chr1:226359489..226362150,3	K562	blood:
5	chr1:226356179..226357747-chr1:226359489..226362150,2	K562	blood:

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

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

rs_ID	r²[population]
rs10732276	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10799337	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799340	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10915952	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915954	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12032630	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12136759	0.91[MEX][hapmap]
rs1877155	0.83[MEX][hapmap]
rs2306121	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889539	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008192	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs3914142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653718	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653722	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9286997	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9659225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659397	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9660696	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9660874	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9660924	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]
rs9661836	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9662709	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9725308	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725342	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728014	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9728310	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9729232	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9729554	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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
rs9286998	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs9286998	PARP1	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr1:226340400-226369600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:226347000-226369600	Weak transcription	Psoas Muscle	Psoas
4	chr1:226348800-226365200	Weak transcription	NHEK	skin
5	chr1:226349000-226366400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:226349000-226373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:226349400-226369200	Weak transcription	Fetal Heart	heart
8	chr1:226349800-226366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:226350000-226363200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:226350000-226370200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:226350000-226373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:226350600-226363800	Weak transcription	Aorta	Aorta
13	chr1:226350600-226369000	Weak transcription	Hela-S3	cervix
14	chr1:226350800-226369600	Weak transcription	Right Ventricle	heart
15	chr1:226351000-226369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:226352200-226372800	Weak transcription	Fetal Kidney	kidney
17	chr1:226352400-226363200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:226352400-226365200	Weak transcription	HMEC	breast
19	chr1:226352400-226368200	Weak transcription	HSMM	muscle
20	chr1:226352600-226365200	Weak transcription	A549	lung
21	chr1:226352600-226369200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:226352600-226370000	Weak transcription	Fetal Brain Female	brain
23	chr1:226352600-226370400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:226352600-226372200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:226352600-226372400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:226352600-226372800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:226352600-226373000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:226352600-226373400	Weak transcription	Esophagus	oesophagus
29	chr1:226352800-226365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:226352800-226372000	Weak transcription	Colonic Mucosa	Colon
31	chr1:226353000-226363000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:226353000-226369400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:226353000-226369600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:226353000-226370200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:226353000-226372000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:226353200-226365000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:226353200-226365600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:226353200-226369600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:226353200-226372000	Weak transcription	HUVEC	blood vessel
40	chr1:226353400-226372400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:226353600-226363000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:226353600-226363400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:226353600-226368800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:226353600-226369000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:226353600-226369600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:226353600-226369600	Weak transcription	Fetal Lung	lung
47	chr1:226353600-226369800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:226353600-226372000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:226353800-226362800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:226353800-226363200	Weak transcription	NHDF-Ad	bronchial

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