Variant report

Variant	rs182600
Chromosome Location	chr7:65574197-65574198
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65574035..65576249-chr7:65590023..65592857,2	MCF-7	breast:
2	chr7:65567522..65569449-chr7:65572493..65575376,3	K562	blood:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1039664	0.82[AMR][1000 genomes]
rs1061361	0.84[AMR][1000 genomes]
rs10807699	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1134256	0.81[AMR][1000 genomes]
rs11538349	0.81[AMR][1000 genomes]
rs1167613	0.82[AMR][1000 genomes]
rs1177514	0.82[AMR][1000 genomes]
rs12698509	0.82[AMR][1000 genomes]
rs13226598	0.82[AMR][1000 genomes]
rs13308751	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546059	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs160543	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160639	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160642	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160643	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160644	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160646	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160648	0.91[AMR][1000 genomes]
rs160649	0.91[AMR][1000 genomes]
rs160651	0.91[AMR][1000 genomes]
rs160652	0.93[AMR][1000 genomes]
rs160655	0.91[AMR][1000 genomes]
rs160656	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160657	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1626926	0.82[AMR][1000 genomes]
rs1701745	0.82[AMR][1000 genomes]
rs1701750	0.82[AMR][1000 genomes]
rs1701758	0.82[AMR][1000 genomes]
rs1701759	0.82[AMR][1000 genomes]
rs1715235	0.84[AMR][1000 genomes]
rs1723265	0.82[AMR][1000 genomes]
rs1723266	0.84[AMR][1000 genomes]
rs1723267	0.84[AMR][1000 genomes]
rs1723269	0.84[AMR][1000 genomes]
rs1723270	0.84[AMR][1000 genomes]
rs1723272	0.82[AMR][1000 genomes]
rs186378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873494	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs188765	0.84[AMR][1000 genomes]
rs1964692	0.84[AMR][1000 genomes]
rs2243480	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257790	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420170	0.82[AMR][1000 genomes]
rs2420171	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2420172	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2456483	0.82[AMR][1000 genomes]
rs2460422	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460425	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460426	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460431	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2462569	0.82[AMR][1000 genomes]
rs2465120	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2637561	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2658583	0.84[AMR][1000 genomes]
rs2949697	0.82[AMR][1000 genomes]
rs2961102	0.84[AMR][1000 genomes]
rs3105600	0.84[AMR][1000 genomes]
rs313798	0.84[AMR][1000 genomes]
rs313799	0.82[AMR][1000 genomes]
rs313800	0.82[AMR][1000 genomes]
rs313801	0.89[AMR][1000 genomes]
rs313802	0.89[AMR][1000 genomes]
rs313803	0.89[AMR][1000 genomes]
rs313807	0.82[AMR][1000 genomes]
rs313809	0.84[AMR][1000 genomes]
rs313813	0.85[AMR][1000 genomes]
rs313814	0.85[AMR][1000 genomes]
rs313819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313821	0.95[ASN][1000 genomes]
rs313822	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313831	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313832	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313833	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316304	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316315	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs316317	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316318	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316321	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316322	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316325	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316329	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316331	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316332	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs316334	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34032527	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34970380	0.84[AMR][1000 genomes]
rs35268390	0.81[AMR][1000 genomes]
rs35396113	0.84[AMR][1000 genomes]
rs35542501	0.81[AMR][1000 genomes]
rs35679560	0.82[AMR][1000 genomes]
rs36004293	0.81[AMR][1000 genomes]
rs36084489	0.84[AMR][1000 genomes]
rs36127118	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs387676	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392355	0.84[AMR][1000 genomes]
rs402418	0.85[AMR][1000 genomes]
rs403089	0.89[AMR][1000 genomes]
rs4145008	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs419603	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422164	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423187	0.84[AMR][1000 genomes]
rs427044	0.84[AMR][1000 genomes]
rs431076	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431318	0.85[AMR][1000 genomes]
rs437889	0.85[AMR][1000 genomes]
rs4481472	0.84[AMR][1000 genomes]
rs448377	0.84[AMR][1000 genomes]
rs451396	0.84[AMR][1000 genomes]
rs458291	0.87[AMR][1000 genomes]
rs462853	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs465359	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs466983	0.87[AMR][1000 genomes]
rs4718309	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718315	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4718316	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4718317	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55886244	0.82[AMR][1000 genomes]
rs57126451	0.82[AMR][1000 genomes]
rs58207111	0.82[AMR][1000 genomes]
rs59794892	0.81[AMR][1000 genomes]
rs59966766	0.84[AMR][1000 genomes]
rs6460274	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6460277	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6958289	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6959002	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6966322	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6974723	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs709607	0.82[AMR][1000 genomes]
rs73136349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73148097	0.84[AMR][1000 genomes]
rs73150014	0.84[AMR][1000 genomes]
rs7787230	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7804223	0.85[AMR][1000 genomes]
rs780453	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs781141	0.81[AMR][1000 genomes]
rs781142	0.82[AMR][1000 genomes]
rs781149	0.82[AMR][1000 genomes]
rs781150	0.84[AMR][1000 genomes]
rs781153	0.84[AMR][1000 genomes]
rs781154	0.84[AMR][1000 genomes]
rs781155	0.84[AMR][1000 genomes]
rs781156	0.84[AMR][1000 genomes]
rs781157	0.82[AMR][1000 genomes]
rs906134	0.82[AMR][1000 genomes]
rs937108	0.82[AMR][1000 genomes]
rs958550	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9769882	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs182600	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs182600	VKORC1L1	cis	Whole Blood	GTEx
rs182600	GUSB	cis	Whole Blood	GTEx
rs182600	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65565200-65579800	Weak transcription	Spleen	Spleen
2	chr7:65565600-65575200	Weak transcription	Liver	Liver
3	chr7:65565600-65575800	Weak transcription	HMEC	breast
4	chr7:65565600-65575800	Weak transcription	NH-A	brain
5	chr7:65565600-65579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:65565800-65579000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:65565800-65579000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:65565800-65579000	Weak transcription	Fetal Stomach	stomach
9	chr7:65565800-65579400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:65566000-65579000	Weak transcription	Primary T cells from cord blood	blood
11	chr7:65566200-65575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:65566200-65579000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:65566200-65579000	Weak transcription	Brain Substantia Nigra	brain
14	chr7:65566200-65579000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:65566200-65579200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:65569200-65575600	Weak transcription	NHEK	skin
17	chr7:65569400-65575800	Weak transcription	A549	lung
18	chr7:65571400-65575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:65571600-65575800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:65571800-65575800	Weak transcription	Osteobl	bone
21	chr7:65571800-65576000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:65572000-65575800	Weak transcription	NHLF	lung
23	chr7:65572000-65579000	Weak transcription	Brain Angular Gyrus	brain
24	chr7:65572400-65575400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:65572600-65575000	Weak transcription	Fetal Intestine Small	intestine
26	chr7:65572600-65575200	Weak transcription	NHDF-Ad	bronchial
27	chr7:65572600-65575800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:65572600-65576200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:65572800-65575200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:65572800-65575600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:65572800-65575800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:65572800-65575800	Weak transcription	K562	blood
33	chr7:65573000-65579400	Weak transcription	HSMMtube	muscle
34	chr7:65573800-65575600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:65573800-65578800	Weak transcription	Hela-S3	cervix
36	chr7:65573800-65578800	Weak transcription	HepG2	liver

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