Variant report

Variant	rs6708081
Chromosome Location	chr2:9898039-9898040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:9891910..9893733-chr2:9895279..9898420,3	MCF-7	breast:
2	chr2:9897830..9899713-chr2:9900837..9903744,2	K562	blood:
3	chr2:9891163..9893022-chr2:9896031..9898454,2	K562	blood:
4	chr2:9887703..9890322-chr2:9895249..9898241,2	MCF-7	breast:
5	chr2:9897337..9900295-chr2:9937034..9939837,3	K562	blood:
6	chr2:9897831..9899412-chr2:9902196..9904626,2	MCF-7	breast:
7	chr2:9895791..9898200-chr2:9907765..9909723,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YWHAQ-1	chr2:9897625-9899428	XLOC_001982

No data

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10171491	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10176382	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10178017	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10180724	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10200779	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10200869	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10202283	0.85[ASN][1000 genomes]
rs1110317	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1123269	0.80[CEU][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11674642	0.90[JPT][hapmap]
rs11680429	0.91[JPT][hapmap]
rs12475853	0.89[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12476199	0.83[ASN][1000 genomes]
rs12476232	0.81[CEU][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12692393	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12692394	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12996417	0.84[ASN][1000 genomes]
rs13018695	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13028425	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13030983	0.85[CHB][hapmap]
rs13395171	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13398163	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13398193	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13398304	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554107	0.85[ASN][1000 genomes]
rs1554108	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357263	0.91[JPT][hapmap]
rs4668636	0.91[JPT][hapmap]
rs4668637	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4668644	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669427	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669428	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669429	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4669445	0.95[JPT][hapmap]
rs4669451	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432033	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs6713497	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6735280	0.91[JPT][hapmap]
rs6740013	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6742929	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6743152	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754662	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6756567	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761286	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761920	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7423455	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7423458	0.85[ASN][1000 genomes]
rs7602784	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs7605675	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs868442	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs884881	0.86[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6708081	PDIA6	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9892400-9898600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:9893600-9898200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:9894600-9899800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:9894800-9898200	Weak transcription	Pancreas	Pancrea
5	chr2:9894800-9899600	Enhancers	Esophagus	oesophagus
6	chr2:9895200-9898800	Weak transcription	A549	lung
7	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
8	chr2:9895600-9900000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:9895600-9900200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:9895600-9900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:9896200-9901400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:9896800-9898600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr2:9896800-9899600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:9896800-9899800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr2:9897000-9898200	Enhancers	Spleen	Spleen
16	chr2:9897000-9898600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:9897000-9898600	Enhancers	Lung	lung
18	chr2:9897000-9899000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:9897000-9902200	Enhancers	K562	blood
20	chr2:9897200-9898200	Bivalent Enhancer	Placenta	Placenta
21	chr2:9897200-9898400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:9897200-9898400	Flanking Active TSS	Osteobl	bone
23	chr2:9897200-9898600	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr2:9897200-9899000	Enhancers	HSMM	muscle
25	chr2:9897200-9899200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:9897400-9898400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr2:9897400-9898400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:9897400-9898400	Weak transcription	HMEC	breast
29	chr2:9897400-9898600	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr2:9897400-9898600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:9897400-9898600	Enhancers	Fetal Brain Male	brain
32	chr2:9897400-9898600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:9897400-9898600	Enhancers	Thymus	Thymus
34	chr2:9897400-9898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:9897400-9899200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:9897600-9898200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:9897600-9898200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
38	chr2:9897600-9898200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:9897600-9898200	Active TSS	Brain Cingulate Gyrus	brain
40	chr2:9897600-9898200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr2:9897600-9898200	Flanking Active TSS	NHLF	lung
42	chr2:9897600-9898400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:9897600-9898400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:9897600-9898400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:9897600-9898400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr2:9897600-9898400	Flanking Active TSS	NH-A	brain
47	chr2:9897600-9898600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:9897600-9898600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:9897600-9898600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr2:9897600-9898600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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