Variant report

Variant	rs1473236
Chromosome Location	chr7:128880831-128880832
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1000676	0.81[JPT][hapmap]
rs10248810	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs10257620	0.83[ASN][1000 genomes]
rs10954224	0.95[ASN][1000 genomes]
rs10954226	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10954230	0.81[JPT][hapmap]
rs11763056	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11763325	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11769045	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11979476	0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs12111832	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12112374	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12534372	0.81[JPT][hapmap]
rs12540568	0.81[JPT][hapmap]
rs12667132	0.81[JPT][hapmap]
rs13235668	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13235749	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13238161	0.90[ASN][1000 genomes]
rs1526900	0.86[JPT][hapmap]
rs1559486	0.90[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs17168512	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1880854	0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2012919	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2056694	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2103232	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2141075	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2402945	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2566876	0.84[ASN][1000 genomes]
rs2566877	0.83[ASN][1000 genomes]
rs2694572	0.82[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs2694574	1.00[JPT][hapmap]
rs2718083	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2718084	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718086	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2718115	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896415	0.94[ASN][1000 genomes]
rs4440569	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4728163	0.81[JPT][hapmap]
rs4728164	0.81[JPT][hapmap]
rs4731566	0.95[ASN][1000 genomes]
rs4731568	0.88[ASN][1000 genomes]
rs4731572	0.81[JPT][hapmap]
rs55638303	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56026912	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59659852	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60275163	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62480596	0.94[ASN][1000 genomes]
rs6467233	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6467235	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66538149	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66864889	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66970518	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67520056	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs67820265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67853067	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67997229	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68076553	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6942756	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6948252	0.84[EUR][1000 genomes]
rs6949950	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6966595	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap]
rs6971917	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6974155	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6980385	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs721691	0.89[ASN][1000 genomes]
rs73472312	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7778277	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7780886	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788327	0.82[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs7792317	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7803052	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806089	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7811141	0.89[ASN][1000 genomes]
rs822038	0.95[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap]
rs822040	0.95[CEU][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs891545	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963465	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9640854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641846	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9641849	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1031284	chr7:128866118-128910506	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473236	COPG2	cis	cerebellum	SCAN
rs1473236	KCP	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128866000-128902200	Weak transcription	Gastric	stomach
2	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
3	chr7:128866400-128891400	Weak transcription	Fetal Stomach	stomach
4	chr7:128866400-128899000	Weak transcription	Ovary	ovary
5	chr7:128866600-128901400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:128866800-128889600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:128867000-128884200	Weak transcription	Primary T cells from cord blood	blood
8	chr7:128867000-128898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:128867600-128885600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:128868600-128897200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:128872800-128892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:128876400-128889800	Weak transcription	Fetal Intestine Small	intestine
14	chr7:128876600-128882000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:128878800-128881400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:128878800-128897000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr7:128879600-128882800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:128880000-128881000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:128880200-128881000	Enhancers	Brain Cingulate Gyrus	brain
20	chr7:128880400-128881200	Enhancers	Brain Anterior Caudate	brain
21	chr7:128880400-128889800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:128880600-128883800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:128880600-128887000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:128880800-128881000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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