Variant report

Variant	rs12662559
Chromosome Location	chr6:110508696-110508697
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:110506447..110509996-chr6:110510060..110514287,5	K562	blood:
2	chr6:110481649..110484031-chr6:110507011..110509592,2	K562	blood:
3	chr6:110500660..110503005-chr6:110505230..110508841,5	MCF-7	breast:
4	chr6:110506402..110508834-chr6:110513795..110516786,2	K562	blood:
5	chr6:110500493..110502758-chr6:110507335..110510018,2	MCF-7	breast:
6	chr6:110499664..110503910-chr6:110507183..110512081,7	K562	blood:
7	chr6:110508464..110511221-chr6:110517530..110521627,4	K562	blood:

Variant related genes	Relation type
ENSG00000168438	Chromatin interaction
ENSG00000112290	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12660108	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12662027	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12662099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664024	0.87[EUR][1000 genomes]
rs12664697	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665152	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665650	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1350943	0.87[EUR][1000 genomes]
rs1350944	0.87[EUR][1000 genomes]
rs1381688	0.87[EUR][1000 genomes]
rs2002631	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2361500	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2885293	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806158	0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs3828928	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41288574	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41288576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57771959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58100980	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58965432	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59181827	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60105161	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61494781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904509	0.86[ASN][1000 genomes]
rs6918158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922245	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922536	0.87[EUR][1000 genomes]
rs6926993	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6927464	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937364	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6940347	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941101	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73765657	0.87[EUR][1000 genomes]
rs73765660	0.87[EUR][1000 genomes]
rs73765665	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7752069	0.87[EUR][1000 genomes]
rs7770634	0.87[EUR][1000 genomes]
rs7771649	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7771909	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374151	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9374153	0.87[EUR][1000 genomes]
rs9374154	0.87[EUR][1000 genomes]
rs9374155	0.87[EUR][1000 genomes]
rs9374157	0.87[EUR][1000 genomes]
rs9386877	0.87[EUR][1000 genomes]
rs9386879	0.87[EUR][1000 genomes]
rs9400361	0.87[EUR][1000 genomes]
rs9487320	0.82[ASN][1000 genomes]
rs9487324	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][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	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1801843	chr6:110506109-110566328	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110502600-110515000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:110502600-110533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:110502600-110536600	Weak transcription	Esophagus	oesophagus
4	chr6:110502800-110513800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:110502800-110533400	Weak transcription	HSMMtube	muscle
6	chr6:110503200-110511600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:110503200-110511800	Weak transcription	Right Ventricle	heart
8	chr6:110503200-110514800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:110503200-110515000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:110503200-110531400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:110503200-110533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:110503400-110509000	Enhancers	Liver	Liver
13	chr6:110503400-110512000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:110503400-110515000	Weak transcription	Placenta	Placenta
15	chr6:110503400-110515000	Weak transcription	NH-A	brain
16	chr6:110503400-110530600	Weak transcription	Fetal Kidney	kidney
17	chr6:110503400-110536600	Weak transcription	Gastric	stomach
18	chr6:110503600-110514400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:110503600-110514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:110503600-110514400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:110503600-110515200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:110503800-110509800	Weak transcription	HSMM	muscle
23	chr6:110503800-110515400	Weak transcription	Fetal Intestine Large	intestine
24	chr6:110503800-110532800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:110503800-110533400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:110504200-110514400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:110504400-110509600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:110504400-110514800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:110504400-110536600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:110504600-110509600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:110504600-110513800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:110504600-110513800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:110504600-110514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:110504600-110519400	Weak transcription	Fetal Intestine Small	intestine
35	chr6:110504600-110532400	Weak transcription	HMEC	breast
36	chr6:110504600-110536600	Weak transcription	Fetal Stomach	stomach
37	chr6:110504800-110509800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:110504800-110509800	Weak transcription	NHDF-Ad	bronchial
39	chr6:110504800-110511000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:110504800-110511600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:110504800-110511800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:110504800-110511800	Weak transcription	Left Ventricle	heart
43	chr6:110504800-110511800	Weak transcription	Lung	lung
44	chr6:110504800-110511800	Weak transcription	Psoas Muscle	Psoas
45	chr6:110504800-110511800	Weak transcription	Right Atrium	heart
46	chr6:110504800-110512800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:110504800-110514200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:110504800-110514400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:110504800-110514400	Weak transcription	Fetal Thymus	thymus
50	chr6:110504800-110514800	Weak transcription	Muscle Satellite Cultured Cells	--

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