Variant report

Variant	rs9374786
Chromosome Location	chr6:119674503-119674504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:119674426-119674528	K562	blood:	n/a	n/a

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

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

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1005506	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs11153815	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526344	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528127	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12529667	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530171	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295374	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295375	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1295380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295394	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342313	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1418376	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555684	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs171843	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs195047	0.84[ASN][1000 genomes]
rs195049	0.83[ASN][1000 genomes]
rs195050	0.83[AMR][1000 genomes]
rs195053	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs195054	0.88[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195055	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195057	0.88[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs195060	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs195061	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs195065	0.90[ASN][1000 genomes]
rs195067	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs195068	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs195069	0.90[ASN][1000 genomes]
rs195070	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs195072	0.87[ASN][1000 genomes]
rs195073	0.90[ASN][1000 genomes]
rs195074	0.90[ASN][1000 genomes]
rs195077	0.88[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs195082	0.90[ASN][1000 genomes]
rs195084	0.90[ASN][1000 genomes]
rs195086	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs195087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs195093	0.83[ASN][1000 genomes]
rs2064161	0.81[AMR][1000 genomes]
rs2066350	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142885	0.81[JPT][hapmap]
rs2295203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299884	0.81[JPT][hapmap]
rs28364655	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778110	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798655	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945638	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4946416	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56095132	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569059	1.00[ASW][hapmap]
rs6569062	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs66524742	0.83[ASN][1000 genomes]
rs6900388	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925366	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932066	0.83[ASN][1000 genomes]
rs6933961	0.81[CHB][hapmap]
rs72952933	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72952941	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7775421	0.80[JPT][hapmap]
rs885028	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9320684	0.81[JPT][hapmap]
rs9372528	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9372531	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9372534	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374784	0.86[AMR][1000 genomes]
rs9374785	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374789	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];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9374790	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385071	0.90[AMR][1000 genomes]
rs9387645	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387647	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387650	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398506	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9398507	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398508	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9398509	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401136	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs9489650	0.83[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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119671800-119689200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:119672000-119674600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:119672000-119675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:119672200-119674600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:119672200-119674600	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:119672200-119675000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:119672400-119674600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:119672400-119675600	Enhancers	Fetal Kidney	kidney
9	chr6:119672400-119675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:119672400-119676200	Enhancers	Primary B cells from cord blood	blood
11	chr6:119673200-119674600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:119673400-119676000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:119673400-119676200	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:119673400-119677200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:119673400-119678200	Weak transcription	NHDF-Ad	bronchial
16	chr6:119673400-119690000	Weak transcription	K562	blood
17	chr6:119673600-119675400	Enhancers	Dnd41	blood
18	chr6:119673600-119680800	Weak transcription	Fetal Heart	heart
19	chr6:119673600-119687200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:119674000-119675400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:119674200-119674600	Enhancers	Adipose Nuclei	Adipose
22	chr6:119674200-119674600	Enhancers	HepG2	liver
23	chr6:119674400-119674600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:119674400-119674600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:119674400-119674600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr6:119674400-119674600	Enhancers	Psoas Muscle	Psoas
27	chr6:119674400-119674800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr6:119674400-119674800	Enhancers	Small Intestine	intestine
29	chr6:119674400-119675200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:119674400-119675200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:119674400-119675200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:119674400-119675200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:119674400-119675200	Enhancers	Brain Anterior Caudate	brain
34	chr6:119674400-119675400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:119674400-119675400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:119674400-119675400	Flanking Active TSS	GM12878-XiMat	blood
37	chr6:119674400-119675600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:119674400-119676000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:119674400-119676000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr6:119674400-119677600	Enhancers	Primary monocytes fromperipheralblood	blood

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