Variant report

Variant	rs9403523
Chromosome Location	chr6:144004981-144004982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143999802..144002439-chr6:144003209..144005357,2	MCF-7	breast:
2	chr6:144000686..144002814-chr6:144004185..144006059,2	K562	blood:
3	chr6:143998230..144000986-chr6:144001245..144005130,4	K562	blood:
4	chr6:144004544..144009046-chr6:144017005..144020189,4	K562	blood:
5	chr6:144002192..144005187-chr6:144008261..144010591,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10872562	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108314	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11155315	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11155317	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12195195	0.84[ASN][1000 genomes]
rs12198291	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12201496	0.84[ASN][1000 genomes]
rs12206069	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12207002	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12208927	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12528456	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3924969	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3934959	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6901659	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907410	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913134	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs6915784	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6916245	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7740709	0.94[JPT][hapmap]
rs7741424	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7748882	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7766510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769294	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7772565	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7776119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8180640	0.82[ASN][1000 genomes]
rs9373396	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373397	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9376776	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9376779	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386042	0.85[CHB][hapmap]
rs9386043	0.80[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9390126	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9399458	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403521	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144000000-144005600	Weak transcription	Small Intestine	intestine
2	chr6:144000600-144007800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:144000600-144008800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:144000800-144008000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:144001800-144007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:144001800-144008000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:144001800-144012200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:144002000-144005200	Weak transcription	Right Ventricle	heart
9	chr6:144002000-144007600	Weak transcription	Ovary	ovary
10	chr6:144002000-144007800	Weak transcription	Aorta	Aorta
11	chr6:144002000-144007800	Weak transcription	NHDF-Ad	bronchial
12	chr6:144002000-144008400	Weak transcription	Placenta	Placenta
13	chr6:144002000-144013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:144002200-144007800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:144002200-144008000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:144002400-144005800	Weak transcription	Fetal Lung	lung
17	chr6:144002400-144007800	Weak transcription	Osteobl	bone
18	chr6:144002800-144006800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:144002800-144011200	Weak transcription	Hela-S3	cervix
20	chr6:144003000-144005000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:144003000-144008000	Weak transcription	Right Atrium	heart
22	chr6:144003200-144005000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
23	chr6:144003400-144005800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:144003400-144005800	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr6:144003400-144008000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:144003600-144005400	Weak transcription	Psoas Muscle	Psoas
27	chr6:144003600-144007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:144003600-144007800	Weak transcription	Lung	lung
29	chr6:144003600-144008000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:144003600-144009800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:144003600-144015000	Weak transcription	Esophagus	oesophagus
32	chr6:144003600-144015000	Weak transcription	Gastric	stomach
33	chr6:144003800-144008800	Weak transcription	Fetal Stomach	stomach
34	chr6:144004400-144005800	Enhancers	HUVEC	blood vessel
35	chr6:144004400-144007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:144004400-144008000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:144004400-144010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:144004400-144013000	Weak transcription	Fetal Kidney	kidney
39	chr6:144004600-144008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:144004800-144005200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:144004800-144005200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:144004800-144005600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:144004800-144007800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:144004800-144007800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:144004800-144007800	Weak transcription	Left Ventricle	heart

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