Variant report

Variant	rs6467233
Chromosome Location	chr7:128868656-128868657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128863424..128866182-chr7:128866726..128869206,3	K562	blood:
2	chr7:128867126..128869752-chr7:128870214..128872194,2	MCF-7	breast:
3	chr7:128863588..128866048-chr7:128867908..128870298,3	MCF-7	breast:
4	chr7:128862977..128866028-chr7:128866480..128869690,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1000676	0.81[JPT][hapmap]
rs10248810	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs10257620	0.82[ASN][1000 genomes]
rs10954224	0.94[ASN][1000 genomes]
rs10954226	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10954230	0.81[JPT][hapmap]
rs11763056	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11763325	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11769045	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11979476	0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs12111832	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12112374	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12534372	0.81[JPT][hapmap]
rs12540568	0.81[JPT][hapmap]
rs12667132	0.81[JPT][hapmap]
rs13235668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13235749	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13238161	0.92[ASN][1000 genomes]
rs1473236	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526900	0.86[JPT][hapmap]
rs1559486	0.90[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs17168512	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1880854	0.87[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2012919	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2056694	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2103232	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2141075	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2402945	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2566876	0.83[ASN][1000 genomes]
rs2566877	0.82[ASN][1000 genomes]
rs2694572	0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2694574	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2718083	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2718084	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718086	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718115	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896415	0.93[ASN][1000 genomes]
rs4440569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4728163	0.81[JPT][hapmap]
rs4728164	0.81[JPT][hapmap]
rs4731566	0.94[ASN][1000 genomes]
rs4731568	0.87[ASN][1000 genomes]
rs4731572	0.81[JPT][hapmap]
rs55638303	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56026912	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59659852	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60275163	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62480596	0.94[ASN][1000 genomes]
rs6467235	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66538149	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs66864889	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66970518	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67520056	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs67820265	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67853067	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67997229	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68076553	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68187585	0.81[EUR][1000 genomes]
rs6942756	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6948252	0.84[EUR][1000 genomes]
rs6949950	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6966595	0.95[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs6971917	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6974155	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6980385	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs721691	0.88[ASN][1000 genomes]
rs73472312	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7778277	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7780886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788327	0.82[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs7792317	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7803052	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806089	0.89[AFR][1000 genomes];0.82[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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963465	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640854	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9641846	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641849	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[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	nsv831127	chr7:128716256-128874691	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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
rs6467233	KCP	cis	cerebellum	SCAN
rs6467233	COPG2	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128865800-128872800	Weak transcription	Lung	lung
2	chr7:128866000-128873600	Weak transcription	Pancreas	Pancrea
3	chr7:128866000-128874400	Weak transcription	HSMM	muscle
4	chr7:128866000-128880000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:128866000-128902200	Weak transcription	Gastric	stomach
6	chr7:128866200-128868800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
8	chr7:128866400-128869400	Weak transcription	HSMMtube	muscle
9	chr7:128866400-128891400	Weak transcription	Fetal Stomach	stomach
10	chr7:128866400-128899000	Weak transcription	Ovary	ovary
11	chr7:128866600-128869600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:128866600-128870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:128866600-128871000	Weak transcription	Adipose Nuclei	Adipose
14	chr7:128866600-128879000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:128866600-128880200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:128866600-128880400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:128866600-128901400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:128866800-128869200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:128866800-128871200	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:128866800-128878000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:128866800-128889600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:128867000-128869000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr7:128867000-128884200	Weak transcription	Primary T cells from cord blood	blood
24	chr7:128867000-128898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:128867200-128869600	Enhancers	Psoas Muscle	Psoas
26	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
27	chr7:128867400-128868800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr7:128867400-128869400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr7:128867400-128869400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:128867400-128869800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:128867600-128868800	Enhancers	Fetal Intestine Small	intestine
32	chr7:128867600-128868800	Enhancers	GM12878-XiMat	blood
33	chr7:128867600-128885600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:128867800-128869000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:128867800-128869800	Enhancers	NHEK	skin
36	chr7:128867800-128878400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:128867800-128880400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:128868000-128869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:128868000-128878400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:128868200-128869200	Weak transcription	HepG2	liver
41	chr7:128868200-128869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:128868200-128869800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:128868200-128872800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:128868200-128875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:128868400-128880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:128868600-128869400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:128868600-128869400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:128868600-128869800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:128868600-128897200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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