Variant report

Variant	rs17400878
Chromosome Location	chr1:10316729-10316730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10864454	0.84[EUR][1000 genomes]
rs11121542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121556	1.00[CHB][hapmap]
rs12119075	1.00[CHB][hapmap]
rs12120465	0.83[EUR][1000 genomes]
rs12120499	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135219	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12137527	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142043	0.84[EUR][1000 genomes]
rs17396340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397129	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762289	0.84[EUR][1000 genomes]
rs4240912	0.84[EUR][1000 genomes]
rs4240913	0.84[EUR][1000 genomes]
rs4846204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846214	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs58036267	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670157	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6679596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6693965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs6702280	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525661	0.84[EUR][1000 genomes]
rs997482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv999251	chr1:10276263-10318163	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv545382	chr1:10309026-10377221	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17400878	KIF1B	Cis_1M	lymphoblastoid	RTeQTL
rs17400878	KIF1B	cis	lymphoblastoid	seeQTL
rs17400878	PTCHD2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10277000-10322000	Weak transcription	Spleen	Spleen
3	chr1:10289200-10317400	Weak transcription	Liver	Liver
4	chr1:10293000-10322000	Weak transcription	Primary T cells from cord blood	blood
5	chr1:10295600-10317600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:10295800-10322000	Weak transcription	Lung	lung
7	chr1:10296400-10316800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:10302000-10321800	Weak transcription	Esophagus	oesophagus
9	chr1:10305200-10317200	Weak transcription	Brain Germinal Matrix	brain
10	chr1:10307600-10340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:10311000-10322000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:10311000-10327600	Weak transcription	Aorta	Aorta
13	chr1:10311400-10321800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:10311400-10322000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:10311600-10331200	Weak transcription	Fetal Thymus	thymus
16	chr1:10311800-10317000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:10311800-10317400	Weak transcription	HUVEC	blood vessel
18	chr1:10312600-10321800	Weak transcription	Hela-S3	cervix
19	chr1:10312600-10327600	Weak transcription	HMEC	breast
20	chr1:10312800-10321800	Weak transcription	NHEK	skin
21	chr1:10312800-10347200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:10313000-10317400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:10313400-10318000	Weak transcription	Stomach Mucosa	stomach
24	chr1:10313400-10320000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:10313400-10327400	Weak transcription	Colonic Mucosa	Colon
26	chr1:10313600-10317400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:10313600-10322200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:10313800-10317200	Weak transcription	Left Ventricle	heart
29	chr1:10313800-10321800	Weak transcription	Pancreas	Pancrea
30	chr1:10313800-10327600	Weak transcription	Right Atrium	heart
31	chr1:10314000-10317600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:10314000-10320000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:10314000-10320000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:10314000-10321800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:10314000-10322000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:10314000-10323600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:10314000-10331800	Weak transcription	K562	blood
38	chr1:10314200-10317000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:10314200-10317000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:10314200-10317400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:10314200-10317400	Weak transcription	A549	lung
42	chr1:10314200-10317600	Weak transcription	Ovary	ovary
43	chr1:10314200-10318600	Weak transcription	Dnd41	blood
44	chr1:10314200-10319600	Weak transcription	Fetal Lung	lung
45	chr1:10314200-10321800	Weak transcription	Right Ventricle	heart
46	chr1:10314200-10322000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:10314200-10323600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:10314200-10356400	Weak transcription	Small Intestine	intestine
49	chr1:10314200-10363400	Weak transcription	Fetal Brain Male	brain
50	chr1:10314400-10317200	Weak transcription	Brain Substantia Nigra	brain

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