Variant report

Variant	rs12209196
Chromosome Location	chr6:36512862-36512863
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36511832..36520020-chr6:36560637..36566762,23	K562	blood:
2	chr6:36511392..36518322-chr6:36560440..36567216,21	MCF-7	breast:
3	chr6:36510774..36513528-chr6:36514327..36515918,2	MCF-7	breast:
4	chr6:36408851..36410684-chr6:36512554..36515336,3	K562	blood:
5	chr6:36511879..36517279-chr6:36558264..36566013,19	MCF-7	breast:
6	chr6:36510007..36526277-chr6:36558145..36566762,35	K562	blood:
7	chr6:36511702..36513578-chr6:36513604..36515650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000112078	Chromatin interaction
ENSG00000179165	Chromatin interaction
ENSG00000112079	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1003249	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10484615	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947607	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947608	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947611	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1137628	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11755264	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756413	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11757842	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759996	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1191	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12110954	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190062	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12211528	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1358981	0.82[EUR][1000 genomes]
rs1535510	0.83[EUR][1000 genomes]
rs16888552	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16888690	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983781	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985423	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007741	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071810	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146333	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2180929	0.83[EUR][1000 genomes]
rs2187827	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239807	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239808	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267925	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267926	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267927	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267928	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267929	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267931	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2267932	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300064	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894407	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752479	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756911	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756912	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3778019	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798470	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798472	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798473	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798474	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819760	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822970	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4598	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55829962	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56086408	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56763433	0.83[EUR][1000 genomes]
rs57423505	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57646047	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58093537	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59104483	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59955083	0.82[EUR][1000 genomes]
rs60043926	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6457920	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6457921	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457922	0.80[EUR][1000 genomes]
rs6457923	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67018593	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67640018	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6899372	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899421	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6899631	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902076	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902473	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905347	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6905686	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6911877	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912117	0.82[EUR][1000 genomes]
rs6912982	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913613	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913693	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913714	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917951	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6917981	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926522	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6926796	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927896	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928087	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6930496	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936942	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6939445	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6941593	0.83[EUR][1000 genomes]
rs73411055	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73413258	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73413267	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7738604	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7742459	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7745411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752714	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7754363	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7763089	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769765	0.83[EUR][1000 genomes]
rs7771028	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772524	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772800	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs933236	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462185	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462186	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462190	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462193	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470273	0.82[EUR][1000 genomes]
rs9470280	0.84[EUR][1000 genomes]
rs9470289	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470291	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470293	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470294	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470295	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470296	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470297	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470300	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470302	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470304	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9767243	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9767778	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv5260	chr6:36471464-36516119	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209196	KCTD20	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36463800-36513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:36478400-36513600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:36478400-36514000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:36479600-36514400	Weak transcription	Spleen	Spleen
5	chr6:36484600-36514000	Weak transcription	Pancreas	Pancrea
6	chr6:36488800-36513800	Weak transcription	Aorta	Aorta
7	chr6:36492400-36514000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:36496000-36513400	Weak transcription	Psoas Muscle	Psoas
9	chr6:36496200-36514200	Weak transcription	Gastric	stomach
10	chr6:36500000-36514000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:36508000-36513400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:36508000-36513600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:36508000-36513600	Weak transcription	Brain Substantia Nigra	brain
14	chr6:36508200-36513600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:36508400-36513200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:36508400-36513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:36508400-36513400	Weak transcription	Fetal Brain Female	brain
18	chr6:36508400-36513600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:36508600-36513400	Weak transcription	NH-A	brain
20	chr6:36508600-36513600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:36508800-36513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:36509000-36514000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:36509200-36513400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:36509200-36513800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:36509600-36513200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:36509600-36513400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:36510200-36513400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:36510600-36513200	Enhancers	Colon Smooth Muscle	Colon
29	chr6:36510600-36514200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:36511000-36513000	Enhancers	Left Ventricle	heart
31	chr6:36511200-36513200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:36511200-36513200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr6:36511200-36513800	Enhancers	Stomach Mucosa	stomach
34	chr6:36511200-36514200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr6:36511400-36513400	Enhancers	Fetal Thymus	thymus
36	chr6:36511600-36513400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:36511600-36513400	Enhancers	Liver	Liver
38	chr6:36511600-36513400	Enhancers	Fetal Heart	heart
39	chr6:36511600-36513800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr6:36511600-36514800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:36511800-36513600	Enhancers	Fetal Brain Male	brain
42	chr6:36512000-36513400	Enhancers	Brain Germinal Matrix	brain
43	chr6:36512000-36513600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:36512000-36513600	Enhancers	Fetal Lung	lung
45	chr6:36512000-36513600	Enhancers	NHEK	skin
46	chr6:36512000-36513800	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr6:36512200-36513000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr6:36512200-36513000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:36512200-36513000	Enhancers	Brain Angular Gyrus	brain
50	chr6:36512200-36513400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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