Variant report

Variant	rs6790867
Chromosome Location	chr3:178738432-178738433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178734474..178738470-chr3:179037032..179039856,4	K562	blood:
2	chr3:178737773..178739885-chr3:179056978..179059649,2	K562	blood:
3	chr3:178735573..178738499-chr3:179040054..179042168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121864	Chromatin interaction
ENSG00000260743	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11711320	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720081	0.91[EUR][1000 genomes]
rs1542	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2677770	0.93[GIH][hapmap]
rs2699887	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs2699905	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs4245914	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4279147	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280676	0.91[EUR][1000 genomes]
rs4315724	0.91[EUR][1000 genomes]
rs4337680	0.91[EUR][1000 genomes]
rs4377525	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395442	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4417911	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425305	0.88[ASN][1000 genomes]
rs4469018	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501160	0.91[EUR][1000 genomes]
rs4505756	0.91[EUR][1000 genomes]
rs4522816	0.89[EUR][1000 genomes]
rs4525914	0.88[EUR][1000 genomes]
rs4552405	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4579062	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607155	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626139	0.91[EUR][1000 genomes]
rs4632588	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955796	0.91[EUR][1000 genomes]
rs4955802	0.89[EUR][1000 genomes]
rs4955807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115013	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56154408	0.89[EUR][1000 genomes]
rs6443607	0.88[EUR][1000 genomes]
rs6443614	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443617	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443618	0.88[AMR][1000 genomes]
rs6772028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784495	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs6789706	0.87[EUR][1000 genomes]
rs6793769	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793893	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794165	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6794956	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795238	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800015	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7429173	0.91[EUR][1000 genomes]
rs7612363	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs7639391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643052	0.89[EUR][1000 genomes]
rs7651510	0.91[EUR][1000 genomes]
rs7652668	0.90[EUR][1000 genomes]
rs7652946	0.91[EUR][1000 genomes]
rs9830482	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831543	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9835752	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835765	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846511	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9860318	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860749	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878734	0.97[ASN][1000 genomes]
rs9879637	0.91[EUR][1000 genomes]
rs9880749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968179	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1009143	chr3:178731525-178783915	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv1799481	chr3:178733212-178782021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6790867	ATP11B	cis	parietal	SCAN
rs6790867	YEATS2	cis	cerebellum	SCAN
rs6790867	KCNMB3	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
2	chr3:178717400-178744400	Weak transcription	HMEC	breast
3	chr3:178722200-178751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:178723400-178749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:178723800-178754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:178731400-178744400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:178732600-178744200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:178733000-178738600	Weak transcription	NH-A	brain
9	chr3:178733400-178751400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:178733800-178742000	Weak transcription	Liver	Liver
11	chr3:178733800-178754600	Weak transcription	Lung	lung
12	chr3:178734000-178755200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:178734000-178755400	Weak transcription	HepG2	liver
14	chr3:178735000-178742200	Weak transcription	NHDF-Ad	bronchial
15	chr3:178735000-178742800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:178735000-178742800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:178735000-178763800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:178735600-178744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:178735600-178745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:178735800-178751600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:178736000-178739400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:178736000-178741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:178736200-178744400	Weak transcription	NHLF	lung
24	chr3:178737400-178739200	Enhancers	Primary T cells from cord blood	blood
25	chr3:178737400-178739800	Genic enhancers	GM12878-XiMat	blood
26	chr3:178737600-178738600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:178737600-178738600	Enhancers	Brain Angular Gyrus	brain
28	chr3:178737600-178738600	Enhancers	Fetal Lung	lung
29	chr3:178737600-178738800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:178737600-178738800	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:178737600-178738800	Enhancers	Brain Hippocampus Middle	brain
32	chr3:178737600-178739200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:178737600-178739200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:178737600-178739600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:178737600-178739600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:178737600-178739800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:178737600-178740000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:178737600-178740000	Enhancers	HUVEC	blood vessel
39	chr3:178737600-178740200	Genic enhancers	HSMMtube	muscle
40	chr3:178737800-178738800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:178737800-178738800	Enhancers	Brain Substantia Nigra	brain
42	chr3:178737800-178739200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:178737800-178739400	Enhancers	Colon Smooth Muscle	Colon
44	chr3:178737800-178739800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr3:178737800-178739800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:178738000-178738600	Enhancers	Aorta	Aorta
47	chr3:178738000-178738600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr3:178738000-178738600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:178738000-178738600	Enhancers	Fetal Stomach	stomach
50	chr3:178738000-178738600	Enhancers	Fetal Thymus	thymus

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