Variant report

Variant	rs12987686
Chromosome Location	chr2:178195609-178195610
allele	G/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:178127878..178129847-chr2:178194449..178197899,4	K562	blood:
2	chr2:178127258..178130407-chr2:178194593..178198613,8	MCF-7	breast:
3	chr2:178193614..178195884-chr2:178197245..178198931,2	K562	blood:
4	chr2:178127949..178131431-chr2:178195364..178200597,7	K562	blood:
5	chr2:178082138..178084856-chr2:178193629..178195873,2	K562	blood:
6	chr2:178130191..178133035-chr2:178195171..178199056,3	K562	blood:
7	chr2:178076403..178078756-chr2:178195004..178198719,3	K562	blood:
8	chr2:178194609..178196529-chr2:178256151..178258954,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000170144	Chromatin interaction
ENSG00000263721	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000229337	Chromatin interaction
ENSG00000018510	Chromatin interaction
ENSG00000213963	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10166244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173008	0.91[EUR][1000 genomes]
rs10173159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10173172	0.91[EUR][1000 genomes]
rs10176724	1.00[CHD][hapmap]
rs10176950	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179735	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10179975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182714	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10196753	0.90[EUR][1000 genomes]
rs10196915	0.90[EUR][1000 genomes]
rs10207932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930782	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10930784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930785	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs10930786	0.91[EUR][1000 genomes]
rs1135118	1.00[CHB][hapmap]
rs11674864	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11681133	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889478	0.90[EUR][1000 genomes]
rs12468046	1.00[CHD][hapmap]
rs12621156	1.00[CHD][hapmap]
rs12623239	0.94[CEU][hapmap]
rs12693118	0.91[EUR][1000 genomes]
rs12693119	0.88[EUR][1000 genomes]
rs12992747	0.90[EUR][1000 genomes]
rs13001890	0.94[CEU][hapmap]
rs13002088	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017003	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017227	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349762	1.00[CHD][hapmap]
rs1377491	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs1453376	0.94[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1463288	0.94[CEU][hapmap]
rs1466208	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs1551288	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs1551289	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs1597959	0.94[CEU][hapmap]
rs17326999	1.00[CHD][hapmap]
rs1869357	0.90[EUR][1000 genomes]
rs1869358	0.89[EUR][1000 genomes]
rs1901828	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs2167903	1.00[CHD][hapmap]
rs2167904	0.94[CEU][hapmap]
rs2178017	1.00[CHD][hapmap]
rs2364733	0.94[CEU][hapmap];0.87[ASN][1000 genomes]
rs2364847	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2364848	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364849	1.00[CHD][hapmap]
rs2444563	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs2602527	0.94[CEU][hapmap]
rs2602528	0.94[CEU][hapmap]
rs2706143	0.94[CEU][hapmap]
rs2706145	0.94[CEU][hapmap]
rs2706146	0.94[CEU][hapmap]
rs2706147	0.94[CEU][hapmap]
rs2706156	0.94[CEU][hapmap]
rs2706158	0.92[CEU][hapmap]
rs2706162	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs4130304	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893827	1.00[CHD][hapmap]
rs4893930	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6414095	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433661	0.87[EUR][1000 genomes]
rs6433662	0.90[EUR][1000 genomes]
rs6433672	1.00[CHD][hapmap]
rs6719278	0.90[EUR][1000 genomes]
rs6720483	1.00[CHD][hapmap]
rs6721168	1.00[CHD][hapmap]
rs6731409	0.90[EUR][1000 genomes]
rs6732113	0.90[EUR][1000 genomes]
rs6732256	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs6746113	0.81[ASN][1000 genomes]
rs6754660	1.00[CHD][hapmap]
rs73039071	0.81[ASN][1000 genomes]
rs73039075	0.81[ASN][1000 genomes]
rs7559715	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs7563082	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7566319	0.81[ASN][1000 genomes]
rs7573583	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs7575328	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588444	0.90[EUR][1000 genomes]
rs7608135	1.00[CHB][hapmap]
rs9288001	1.00[CHD][hapmap]
rs952034	0.94[CEU][hapmap]
rs9941681	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3051	chr2:178193436-178239394	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12987686	PDE11A	cis	parietal	SCAN
rs12987686	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178160800-178196200	Weak transcription	Ovary	ovary
2	chr2:178175200-178203000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:178179200-178196600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:178179800-178196800	Weak transcription	Fetal Brain Female	brain
5	chr2:178179800-178196800	Weak transcription	Osteobl	bone
6	chr2:178180400-178196400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:178180800-178196400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:178182400-178196800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:178182800-178196600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:178184000-178196400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:178184400-178196600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:178184800-178196800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:178187400-178196800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:178187400-178196800	Weak transcription	Esophagus	oesophagus
15	chr2:178187600-178196400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:178187600-178196800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:178187600-178216400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:178187800-178196600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:178187800-178196600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:178187800-178196600	Weak transcription	Brain Anterior Caudate	brain
21	chr2:178187800-178196600	Weak transcription	Brain Substantia Nigra	brain
22	chr2:178187800-178196800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:178187800-178210800	Weak transcription	Left Ventricle	heart
24	chr2:178187800-178216400	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:178188000-178196400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:178188000-178196400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:178188000-178196600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:178188000-178196600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:178188000-178196600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:178188000-178196800	Weak transcription	Primary B cells from cord blood	blood
31	chr2:178188000-178196800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:178188000-178196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:178188000-178196800	Weak transcription	Fetal Stomach	stomach
34	chr2:178188000-178196800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:178188200-178196400	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:178188200-178196600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:178190600-178202600	Weak transcription	NHDF-Ad	bronchial
38	chr2:178191000-178196400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:178191000-178196600	Weak transcription	Fetal Heart	heart
40	chr2:178191000-178196600	Weak transcription	HSMM	muscle
41	chr2:178191000-178200400	Weak transcription	Small Intestine	intestine
42	chr2:178191200-178196600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:178191200-178196600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:178191400-178196600	Weak transcription	Fetal Kidney	kidney
45	chr2:178191400-178196600	Weak transcription	NHLF	lung
46	chr2:178191400-178196800	Weak transcription	Aorta	Aorta
47	chr2:178191600-178202800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:178191800-178196600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:178191800-178196600	Weak transcription	HSMMtube	muscle
50	chr2:178192000-178201800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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