Variant report

Variant	rs887061
Chromosome Location	chr2:234764618-234764619
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234761541-234765493	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234287841..234290274-chr2:234763393..234765427,2	MCF-7	breast:
2	chr2:234763499..234765002-chr2:234766647..234768306,2	MCF-7	breast:
3	chr2:234764614..234767781-chr2:234770318..234773555,4	MCF-7	breast:
4	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000201013	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1003540	0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10166942	0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10170399	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10187654	0.93[ASN][1000 genomes]
rs10929309	0.96[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10929312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11563063	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11563066	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11563227	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892538	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12997802	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016127	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016553	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1392606	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965629	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1985366	0.90[ASN][1000 genomes]
rs2159200	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286430	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286431	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2302155	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2361506	0.81[GIH][hapmap]
rs2362290	0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732215	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4233636	0.81[ASN][1000 genomes]
rs4663983	0.91[ASN][1000 genomes]
rs4663986	0.81[ASN][1000 genomes]
rs6431648	0.82[ASN][1000 genomes]
rs6709005	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6738979	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6760630	0.93[ASN][1000 genomes]
rs737636	0.82[ASN][1000 genomes]
rs7567475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604471	0.80[ASN][1000 genomes]
rs917432	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs917433	0.93[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917434	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968402	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs990418	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs887061	NCL	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234763600-234776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:234763800-234765000	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:234763800-234766000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:234763800-234766000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:234763800-234766200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:234763800-234774600	Weak transcription	Placenta	Placenta
7	chr2:234763800-234774800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:234763800-234775200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:234763800-234775400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:234763800-234776600	Weak transcription	Right Ventricle	heart
11	chr2:234764000-234764800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:234764000-234765800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:234764000-234766000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:234764000-234766000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:234764000-234766000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:234764000-234766000	Weak transcription	Stomach Mucosa	stomach
17	chr2:234764000-234766000	Enhancers	K562	blood
18	chr2:234764000-234766000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:234764000-234766200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:234764000-234774400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:234764000-234775200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:234764000-234776400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:234764000-234776600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:234764000-234776600	Weak transcription	HUVEC	blood vessel
25	chr2:234764200-234764800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:234764200-234766000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:234764200-234766000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:234764200-234766000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:234764200-234766000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:234764200-234766000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:234764200-234766200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:234764200-234766200	Weak transcription	Thymus	Thymus
33	chr2:234764200-234766400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:234764200-234766400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:234764200-234766400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:234764200-234766400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:234764200-234766400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:234764200-234766400	Weak transcription	GM12878-XiMat	blood
39	chr2:234764200-234770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:234764200-234771000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:234764200-234773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:234764200-234774200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:234764200-234774400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:234764200-234774600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:234764200-234774800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:234764200-234774800	Weak transcription	Osteobl	bone
47	chr2:234764200-234775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:234764200-234775200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:234764200-234776600	Weak transcription	Primary B cells from cord blood	blood
50	chr2:234764200-234776600	Weak transcription	Primary T cells from cord blood	blood

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