Variant report

Variant	rs12524617
Chromosome Location	chr6:119673826-119673827
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:119673691-119673882	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:119673474..119675079-chr6:119676928..119679552,2	K562	blood:
2	chr6:119672022..119674199-chr6:119758005..119760805,2	K562	blood:
3	chr6:119671918..119674788-chr6:119887253..119890815,3	K562	blood:
4	chr6:119668152..119672285-chr6:119673337..119678807,6	MCF-7	breast:
5	chr6:119668881..119671932-chr6:119672214..119675857,4	MCF-7	breast:

No data

Variant related genes	Relation type
MAN1A1	TF binding region
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1022869	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1022870	0.93[ASN][1000 genomes]
rs1028327	0.86[ASN][1000 genomes]
rs1028328	0.86[ASN][1000 genomes]
rs10456921	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10457352	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10457353	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10457355	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457356	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10485001	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10872173	0.86[ASN][1000 genomes]
rs10872177	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153796	0.93[ASN][1000 genomes]
rs11153797	0.93[ASN][1000 genomes]
rs11153800	0.93[ASN][1000 genomes]
rs11153803	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153805	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153808	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153810	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153811	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153812	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11751945	0.93[ASN][1000 genomes]
rs11755967	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759899	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11961647	0.93[ASN][1000 genomes]
rs11962938	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12192420	0.93[ASN][1000 genomes]
rs12198423	0.93[ASN][1000 genomes]
rs12198667	0.93[ASN][1000 genomes]
rs12199883	0.81[ASN][1000 genomes]
rs12200554	0.86[ASN][1000 genomes]
rs12205260	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205826	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12206472	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207595	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12210002	0.80[EUR][1000 genomes]
rs12527248	0.81[ASN][1000 genomes]
rs1295383	0.81[ASN][1000 genomes]
rs1295384	0.81[ASN][1000 genomes]
rs1295388	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797067	0.81[ASN][1000 genomes]
rs2036257	0.81[ASN][1000 genomes]
rs2092218	0.86[ASN][1000 genomes]
rs2144236	0.81[ASN][1000 genomes]
rs35305935	0.81[ASN][1000 genomes]
rs4607463	0.86[ASN][1000 genomes]
rs56827721	0.92[ASN][1000 genomes]
rs61094987	0.92[ASN][1000 genomes]
rs6569056	0.86[ASN][1000 genomes]
rs6569057	0.86[ASN][1000 genomes]
rs6569065	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569066	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569072	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6569073	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569076	0.81[ASN][1000 genomes]
rs6903249	0.93[ASN][1000 genomes]
rs6909928	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913626	0.93[ASN][1000 genomes]
rs6913654	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6915957	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6918913	0.93[ASN][1000 genomes]
rs6920832	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932241	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932292	0.86[ASN][1000 genomes]
rs6935126	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936790	0.81[ASN][1000 genomes]
rs73529045	1.00[ASN][1000 genomes]
rs73529086	1.00[ASN][1000 genomes]
rs73535209	0.84[ASN][1000 genomes]
rs73535254	0.84[ASN][1000 genomes]
rs7740993	0.86[ASN][1000 genomes]
rs7743824	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745295	0.81[ASN][1000 genomes]
rs7745633	0.81[ASN][1000 genomes]
rs7750041	0.93[ASN][1000 genomes]
rs7753492	0.93[ASN][1000 genomes]
rs7754482	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760582	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7763569	0.86[ASN][1000 genomes]
rs7767198	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770777	0.93[ASN][1000 genomes]
rs926859	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9374795	0.81[ASN][1000 genomes]
rs9489697	0.81[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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119671800-119689200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:119672000-119674400	Weak transcription	Small Intestine	intestine
3	chr6:119672000-119674600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:119672000-119675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:119672200-119674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:119672200-119674600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:119672200-119674600	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:119672200-119675000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:119672400-119674400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:119672400-119674400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:119672400-119674400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:119672400-119674400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:119672400-119674600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:119672400-119675600	Enhancers	Fetal Kidney	kidney
15	chr6:119672400-119675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:119672400-119676200	Enhancers	Primary B cells from cord blood	blood
17	chr6:119672600-119674400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:119672600-119674400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:119673200-119674200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:119673200-119674400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:119673200-119674400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:119673200-119674400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:119673200-119674600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:119673400-119674400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:119673400-119676000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:119673400-119676200	Enhancers	Primary hematopoietic stem cells	blood
27	chr6:119673400-119677200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:119673400-119678200	Weak transcription	NHDF-Ad	bronchial
29	chr6:119673400-119690000	Weak transcription	K562	blood
30	chr6:119673600-119674000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:119673600-119674000	Weak transcription	GM12878-XiMat	blood
32	chr6:119673600-119674200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr6:119673600-119675400	Enhancers	Dnd41	blood
34	chr6:119673600-119680800	Weak transcription	Fetal Heart	heart
35	chr6:119673600-119687200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:119673800-119674200	Weak transcription	Adipose Nuclei	Adipose
37	chr6:119673800-119674200	Weak transcription	HepG2	liver

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