Variant report

Variant	rs2298167
Chromosome Location	chr1:151499731-151499732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	1:151171193-151178589..1:151496437-151509688	Hela-S3	cervix:
2	chr1:151271008..151273642-chr1:151498253..151500140,2	MCF-7	breast:
3	chr1:151499502..151502122-chr1:151511648..151513316,2	MCF-7	breast:
4	1:151496437-151509688..1:151592347-151603110	Hela-S3	cervix:
5	chr1:151482538..151486660-chr1:151496961..151502245,5	MCF-7	breast:
6	1:151402394-151411623..1:151496437-151509688	K562	blood:

Variant related genes	Relation type
ENSG00000143367	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000232536	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1009289	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10127622	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10788807	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10788808	0.83[ASN][1000 genomes]
rs10888418	0.83[ASN][1000 genomes]
rs10888419	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11204827	0.91[JPT][hapmap]
rs11204828	0.91[JPT][hapmap]
rs11204834	0.83[ASN][1000 genomes]
rs11204835	0.82[ASN][1000 genomes]
rs11204837	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204839	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583133	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026585	0.86[AMR][1000 genomes]
rs12032983	0.83[ASN][1000 genomes]
rs12037100	0.85[AMR][1000 genomes]
rs12118440	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12128578	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12730114	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1547832	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1573129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573130	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2211435	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs2298168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2337359	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970955	0.91[JPT][hapmap]
rs61261719	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6675984	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548090	0.84[ASN][1000 genomes]
rs7552458	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers 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	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2298167	LCE3E	cis	parietal	SCAN
rs2298167	OTUD7B	cis	cerebellum	SCAN
rs2298167	TUFT1	cis	cerebellum	SCAN
rs2298167	SCNM1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151484600-151512000	Weak transcription	Right Atrium	heart
2	chr1:151485200-151511800	Weak transcription	Fetal Brain Female	brain
3	chr1:151485800-151511800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:151485800-151512200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:151486000-151501800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:151486600-151511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:151486800-151512200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:151487000-151501800	Weak transcription	Esophagus	oesophagus
9	chr1:151487000-151511800	Weak transcription	Small Intestine	intestine
10	chr1:151487200-151502400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:151487400-151501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:151489200-151507000	Weak transcription	NHEK	skin
13	chr1:151489200-151507400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:151491000-151500000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr1:151491000-151505200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:151491600-151509000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:151492000-151507400	Weak transcription	Stomach Mucosa	stomach
18	chr1:151493200-151501000	Weak transcription	HMEC	breast
19	chr1:151493200-151507600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:151493400-151501200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:151493400-151501200	Weak transcription	Colonic Mucosa	Colon
22	chr1:151493400-151501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:151493400-151511800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:151493400-151511800	Weak transcription	Ovary	ovary
25	chr1:151493400-151512200	Weak transcription	Fetal Kidney	kidney
26	chr1:151493600-151511200	Strong transcription	Fetal Intestine Large	intestine
27	chr1:151494400-151511800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:151495200-151506200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:151495400-151511200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:151495400-151511400	Strong transcription	Liver	Liver
31	chr1:151495600-151499800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:151495600-151500400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:151495600-151505000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:151495600-151511000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:151495800-151500200	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:151495800-151500200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:151495800-151503000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:151496400-151499800	Strong transcription	Pancreas	Pancrea
39	chr1:151496600-151499800	Strong transcription	Brain Angular Gyrus	brain
40	chr1:151496600-151500400	Strong transcription	Fetal Stomach	stomach
41	chr1:151497000-151501400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:151497600-151510200	Strong transcription	Fetal Intestine Small	intestine
43	chr1:151498000-151511800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:151498200-151501600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:151498200-151501800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:151498200-151502000	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:151498200-151502000	Weak transcription	Brain Substantia Nigra	brain
48	chr1:151498200-151505800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:151498200-151508800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:151498400-151501200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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