Variant report

Variant	rs2068871
Chromosome Location	chr1:173796169-173796170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
2	chr1:173397836..173400483-chr1:173795399..173797662,2	K562	blood:
3	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
4	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:
5	chr1:173794991..173797000-chr1:174191375..174193794,2	K562	blood:
6	chr1:173765402..173769315-chr1:173795358..173797976,3	K562	blood:
7	chr1:173796125..173798114-chr1:173834469..173837018,2	MCF-7	breast:
8	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
9	chr1:173794468..173797418-chr1:173804249..173806445,2	MCF-7	breast:
10	chr1:173791090..173796578-chr1:173835400..173838797,13	MCF-7	breast:
11	chr1:173386417..173388679-chr1:173795468..173797775,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16846418	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846478	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846526	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846593	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2065170	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227589	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2227592	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235095	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2759328	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791021	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57022387	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58977252	0.86[AFR][1000 genomes]
rs58994962	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61262741	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61649485	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656255	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685043	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs6696381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941987	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs941988	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9970048	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2068871	CENPL	cis	lymphoblastoid	seeQTL
rs2068871	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794200-173804000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:173794400-173802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:173794400-173806800	Weak transcription	Spleen	Spleen
4	chr1:173794400-173812600	Weak transcription	Small Intestine	intestine
5	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
6	chr1:173794600-173796200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:173794600-173797600	Weak transcription	NHDF-Ad	bronchial
8	chr1:173794600-173799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:173794600-173799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:173794600-173799400	Weak transcription	Left Ventricle	heart
11	chr1:173794600-173799600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:173794600-173799600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:173794600-173799800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:173794600-173799800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:173794600-173799800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:173794600-173799800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:173794600-173799800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:173794600-173799800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:173794600-173799800	Weak transcription	Liver	Liver
20	chr1:173794600-173799800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:173794600-173799800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:173794600-173799800	Weak transcription	Lung	lung
23	chr1:173794600-173799800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:173794600-173800000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:173794600-173803200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:173794600-173804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:173794600-173805200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:173794600-173805800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:173794600-173805800	Weak transcription	NH-A	brain
30	chr1:173794600-173806000	Weak transcription	HSMMtube	muscle
31	chr1:173794600-173808600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:173794600-173809600	Weak transcription	Fetal Kidney	kidney
33	chr1:173794600-173810600	Weak transcription	Ovary	ovary
34	chr1:173794600-173812400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:173794600-173812600	Weak transcription	Aorta	Aorta
36	chr1:173794600-173813000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:173794600-173814600	Weak transcription	Esophagus	oesophagus
38	chr1:173794600-173820600	Weak transcription	NHLF	lung
39	chr1:173794600-173821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:173794600-173821800	Weak transcription	Pancreas	Pancrea
41	chr1:173794600-173822000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
45	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
46	chr1:173794800-173798800	Weak transcription	Fetal Intestine Small	intestine
47	chr1:173794800-173799400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:173794800-173799400	Weak transcription	Fetal Intestine Large	intestine
49	chr1:173794800-173799800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:173794800-173799800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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