Variant report

Variant	rs10257620
Chromosome Location	chr7:128901429-128901430
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128866260..128868499-chr7:128899979..128902017,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1000676	0.81[JPT][hapmap]
rs10248810	0.95[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10954224	0.84[ASN][1000 genomes]
rs10954226	0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs10954230	0.81[JPT][hapmap]
rs11769045	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979476	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12111832	0.97[ASN][1000 genomes]
rs12112374	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs12216567	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12534372	0.81[JPT][hapmap]
rs12540568	0.81[JPT][hapmap]
rs12667132	0.81[JPT][hapmap]
rs13226649	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13235668	0.83[ASN][1000 genomes]
rs13235749	0.83[ASN][1000 genomes]
rs1473236	0.83[ASN][1000 genomes]
rs1526900	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1559486	0.91[JPT][hapmap]
rs1880854	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2012919	0.97[ASN][1000 genomes]
rs2141075	0.82[ASN][1000 genomes]
rs2402944	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2566876	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566885	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2566886	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694572	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2694574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2718083	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2718084	0.81[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718086	0.81[EUR][1000 genomes]
rs2718089	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2718093	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718096	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2718115	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2896415	0.85[ASN][1000 genomes]
rs4728163	0.81[JPT][hapmap]
rs4728164	0.81[JPT][hapmap]
rs4731566	0.84[ASN][1000 genomes]
rs4731572	0.81[JPT][hapmap]
rs55638303	0.85[ASN][1000 genomes]
rs56026912	0.82[EUR][1000 genomes]
rs62480596	0.80[ASN][1000 genomes]
rs6467233	0.87[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs6467237	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6467240	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6467241	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6467242	0.84[EUR][1000 genomes]
rs66970518	0.82[ASN][1000 genomes]
rs67820265	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67853067	0.81[ASN][1000 genomes]
rs68184415	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6942756	0.85[ASN][1000 genomes]
rs6949950	0.81[EUR][1000 genomes]
rs6966595	0.82[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap]
rs6967464	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6974155	0.82[EUR][1000 genomes]
rs6980385	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs7780886	0.83[ASN][1000 genomes]
rs7782348	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7788327	0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7794622	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7811141	0.81[ASN][1000 genomes]
rs822038	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs822040	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs891545	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs963465	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9640854	0.85[ASN][1000 genomes]
rs9641846	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9641849	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	esv3349195	chr7:128887559-128918489	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10257620	COPG2	cis	cerebellum	SCAN
rs10257620	KCP	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128866000-128902200	Weak transcription	Gastric	stomach
2	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
3	chr7:128892600-128914200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:128895800-128902200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:128897400-128914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:128897400-128919400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:128898800-128905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:128898800-128919600	Weak transcription	Right Ventricle	heart
9	chr7:128899000-128901800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:128899000-128911600	Weak transcription	Brain Anterior Caudate	brain
11	chr7:128899200-128902200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:128899200-128902200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:128899200-128902400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:128899200-128909800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:128899400-128913600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:128899600-128901600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:128899600-128902200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:128899600-128902200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr7:128899600-128903000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:128899800-128902000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:128899800-128902200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:128899800-128902200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:128899800-128902200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:128899800-128903800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:128900000-128902000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:128900000-128902000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:128900000-128902000	Weak transcription	GM12878-XiMat	blood
28	chr7:128900000-128902200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:128900000-128902200	Weak transcription	Primary T cells from cord blood	blood
30	chr7:128900000-128902200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr7:128900000-128902200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:128900000-128902200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:128900000-128902200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:128900000-128925000	Weak transcription	Psoas Muscle	Psoas
35	chr7:128900200-128901600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:128900200-128901800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:128900200-128901800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:128900200-128902000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:128900200-128902200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:128900200-128902200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr7:128900200-128902400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr7:128900200-128902400	Weak transcription	NHEK	skin
43	chr7:128900200-128902600	Weak transcription	HMEC	breast
44	chr7:128900200-128902800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:128900400-128901600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:128900600-128901600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:128900600-128901600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:128901000-128902600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr7:128901200-128902400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:128901200-128903400	Enhancers	HUES48 Cell Line	embryonic stem cell

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