Variant report

Variant	rs6572290
Chromosome Location	chr14:45397165-45397166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45396977..45399022-chr14:45400383..45401934,2	MCF-7	breast:
2	chr14:45395985..45398844-chr14:45429401..45432165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198718	Chromatin interaction
ENSG00000179454	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10083439	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10129173	0.96[EUR][1000 genomes]
rs10131066	0.83[EUR][1000 genomes]
rs10131615	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10132389	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs10132547	1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10132949	0.82[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10134071	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10134598	0.88[TSI][hapmap]
rs10135085	0.83[TSI][hapmap]
rs10135890	0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10136008	0.90[EUR][1000 genomes]
rs10136855	0.96[EUR][1000 genomes]
rs10138272	0.89[EUR][1000 genomes]
rs10139998	0.96[EUR][1000 genomes]
rs10140013	0.94[EUR][1000 genomes]
rs10140049	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs10140108	0.98[EUR][1000 genomes]
rs10140222	1.00[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs10140318	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10145092	0.82[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10145267	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs10146395	0.92[EUR][1000 genomes]
rs10147499	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10149484	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs10150646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10152101	0.82[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs10483549	0.82[CHB][hapmap]
rs1053667	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11157423	0.82[CEU][hapmap];0.98[EUR][1000 genomes]
rs11157424	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11844832	0.82[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11845088	0.96[EUR][1000 genomes]
rs11845904	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11845956	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11846656	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11847039	0.89[EUR][1000 genomes]
rs11847336	0.83[TSI][hapmap]
rs11848334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11848799	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11849208	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs11849583	0.96[EUR][1000 genomes]
rs11850363	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs11851218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851357	0.89[EUR][1000 genomes]
rs11851516	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12100842	1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1593279	0.89[EUR][1000 genomes]
rs17115639	0.89[EUR][1000 genomes]
rs17115646	0.89[EUR][1000 genomes]
rs17115648	0.89[EUR][1000 genomes]
rs17115652	0.89[EUR][1000 genomes]
rs17115667	0.82[CHB][hapmap]
rs17115674	0.82[CHB][hapmap];0.88[MEX][hapmap]
rs17115677	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17115680	0.96[YRI][hapmap]
rs17115688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115703	0.82[CEU][hapmap];0.98[EUR][1000 genomes]
rs17115718	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs17115787	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17115809	0.83[TSI][hapmap]
rs17115811	0.83[TSI][hapmap]
rs2295157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2295158	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.94[ASN][1000 genomes]
rs2295160	0.94[ASN][1000 genomes]
rs28432035	0.89[EUR][1000 genomes]
rs28448551	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs28517769	0.96[EUR][1000 genomes]
rs28558522	0.98[EUR][1000 genomes]
rs28572336	0.92[EUR][1000 genomes]
rs28594810	0.92[EUR][1000 genomes]
rs28622413	0.92[EUR][1000 genomes]
rs28681969	0.92[EUR][1000 genomes]
rs28695721	0.98[EUR][1000 genomes]
rs28703636	0.96[EUR][1000 genomes]
rs28756151	0.86[EUR][1000 genomes]
rs2899960	0.96[EUR][1000 genomes]
rs3736747	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825627	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs3825629	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs4141578	0.85[GIH][hapmap]
rs56386358	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56706956	0.92[EUR][1000 genomes]
rs56836063	0.85[EUR][1000 genomes]
rs57129780	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57147026	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57614513	0.92[EUR][1000 genomes]
rs57694277	0.92[EUR][1000 genomes]
rs58013518	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58338525	0.89[EUR][1000 genomes]
rs58920861	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59992752	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60521816	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60595870	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60891427	0.92[EUR][1000 genomes]
rs61707578	0.92[EUR][1000 genomes]
rs6572281	1.00[CHB][hapmap]
rs66488071	0.96[EUR][1000 genomes]
rs66535982	0.96[EUR][1000 genomes]
rs66662385	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67643245	0.96[EUR][1000 genomes]
rs7140739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145831	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7145870	0.82[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7146566	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7147811	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs7151557	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7158846	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7161626	1.00[CHB][hapmap]
rs72474137	0.92[ASN][1000 genomes]
rs73334104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73334114	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73334131	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73334135	0.98[EUR][1000 genomes]
rs73334148	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73334154	0.98[EUR][1000 genomes]
rs73334157	0.98[EUR][1000 genomes]
rs73334162	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73334165	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73334172	0.98[EUR][1000 genomes]
rs73334176	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73334913	0.92[EUR][1000 genomes]
rs73346336	0.94[EUR][1000 genomes]
rs73346344	0.98[EUR][1000 genomes]
rs73346351	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73346360	0.96[EUR][1000 genomes]
rs73348065	0.88[EUR][1000 genomes]
rs73348069	0.92[EUR][1000 genomes]
rs73348076	0.92[EUR][1000 genomes]
rs73348079	0.92[EUR][1000 genomes]
rs73348088	0.92[EUR][1000 genomes]
rs73348095	0.92[EUR][1000 genomes]
rs73348939	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348947	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348950	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73348953	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73348959	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73348966	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348975	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73348977	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348981	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73348987	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73349820	0.85[EUR][1000 genomes]
rs73350201	0.96[EUR][1000 genomes]
rs73352233	0.92[EUR][1000 genomes]
rs73352238	0.89[EUR][1000 genomes]
rs73353644	0.85[EUR][1000 genomes]
rs73353657	0.85[EUR][1000 genomes]
rs7492763	0.82[CHB][hapmap]
rs7493246	0.96[EUR][1000 genomes]
rs7493823	0.92[EUR][1000 genomes]
rs8006685	0.82[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs8011828	0.82[CHB][hapmap]
rs8015453	0.92[EUR][1000 genomes]
rs8018380	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8022008	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs8022608	0.92[EUR][1000 genomes]
rs9323106	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869289	chr14:44752382-45447415	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv901832	chr14:44847444-45415597	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1047886	chr14:45189653-45543182	Strong transcription Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv542079	chr14:45189653-45543182	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1053437	chr14:45232269-45424222	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv1795667	chr14:45361680-45721052	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	esv1794986	chr14:45368685-45650813	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6572290	RP11-398E10.1	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45368200-45397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:45375400-45403000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:45382000-45400600	Weak transcription	Left Ventricle	heart
4	chr14:45382000-45408000	Weak transcription	Pancreas	Pancrea
5	chr14:45383000-45397600	Weak transcription	Liver	Liver
6	chr14:45383000-45405800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:45384400-45406800	Weak transcription	Fetal Muscle Leg	muscle
8	chr14:45384800-45397400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr14:45384800-45408000	Weak transcription	Brain Hippocampus Middle	brain
10	chr14:45386600-45405600	Weak transcription	Fetal Lung	lung
11	chr14:45386800-45405600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:45388400-45398000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:45389600-45406800	Weak transcription	HSMMtube	muscle
14	chr14:45390000-45397400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr14:45390200-45398200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr14:45390200-45406800	Weak transcription	Fetal Stomach	stomach
17	chr14:45390400-45400600	Weak transcription	Primary T cells from cord blood	blood
18	chr14:45390400-45406600	Weak transcription	Brain Germinal Matrix	brain
19	chr14:45390400-45408200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:45390600-45397600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr14:45390600-45408400	Weak transcription	Fetal Brain Female	brain
22	chr14:45391200-45400000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:45391200-45405800	Weak transcription	Fetal Intestine Large	intestine
24	chr14:45391200-45411000	Weak transcription	HSMM	muscle
25	chr14:45391200-45413000	Weak transcription	HUVEC	blood vessel
26	chr14:45391400-45406400	Weak transcription	Fetal Intestine Small	intestine
27	chr14:45391400-45406800	Weak transcription	Thymus	Thymus
28	chr14:45392200-45397400	Weak transcription	Adipose Nuclei	Adipose
29	chr14:45392400-45397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:45393000-45397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:45394200-45413800	Weak transcription	HepG2	liver
32	chr14:45394400-45397600	Weak transcription	NHDF-Ad	bronchial
33	chr14:45394400-45408000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:45394600-45408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr14:45394800-45406800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr14:45395000-45408000	Weak transcription	Gastric	stomach
37	chr14:45395200-45397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr14:45395200-45397600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:45395200-45403000	Weak transcription	GM12878-XiMat	blood
40	chr14:45395200-45403200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:45395200-45403400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr14:45395200-45412400	Weak transcription	Brain Anterior Caudate	brain
43	chr14:45395200-45413800	Weak transcription	Fetal Brain Male	brain
44	chr14:45395400-45397200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr14:45395400-45403200	Weak transcription	Osteobl	bone
46	chr14:45395400-45408000	Weak transcription	Brain Angular Gyrus	brain
47	chr14:45395400-45414400	Weak transcription	NH-A	brain
48	chr14:45395600-45397400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr14:45395600-45397400	Weak transcription	Fetal Thymus	thymus
50	chr14:45395600-45400000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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