Variant report

Variant	rs12475856
Chromosome Location	chr2:9953486-9953487
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:9951629..9954793-chr2:10090886..10093950,3	MCF-7	breast:
2	chr2:9947583..9953611-chr2:9980461..9984922,8	MCF-7	breast:
3	chr2:9951073..9955556-chr2:10089913..10091836,5	MCF-7	breast:
4	chr2:9949012..9952005-chr2:9952060..9955056,3	K562	blood:
5	chr2:9952816..9955217-chr2:10179305..10181124,2	K562	blood:
6	chr2:9952585..9955462-chr2:9959911..9962016,2	MCF-7	breast:
7	chr2:9952171..9953849-chr2:9962646..9965376,2	MCF-7	breast:
8	chr2:9953452..9957551-chr2:10260663..10263596,3	K562	blood:
9	chr2:9951674..9954142-chr2:10158863..10161812,2	MCF-7	breast:
10	chr2:9953287..9954158-chr2:10212428..10212955,2	K562	blood:
11	chr2:9952588..9955831-chr2:9967859..9972229,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171848	Chromatin interaction
ENSG00000260476	Chromatin interaction
ENSG00000134317	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000260077	Chromatin interaction
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10803701	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10803702	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10803704	0.86[CHB][hapmap]
rs11892895	0.87[CHB][hapmap]
rs871277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
6	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
7	nsv524327	chr2:9913515-9954768	Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv873621	chr2:9924387-9954598	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv517701	chr2:9933956-9954768	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv580958	chr2:9942159-9955047	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv528645	chr2:9946213-9975557	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	nsv873622	chr2:9948404-9971366	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv873623	chr2:9949464-9964947	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv873624	chr2:9949464-9971366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv873625	chr2:9949464-9971366	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv469416	chr2:9949464-9975557	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
18	nsv873626	chr2:9949464-9975557	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
19	nsv873627	chr2:9949464-9982608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
20	nsv873628	chr2:9949464-9985670	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
21	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
22	nsv469427	chr2:9951970-9975557	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
23	nsv580959	chr2:9951970-9975557	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9933200-9953800	Weak transcription	Fetal Heart	heart
2	chr2:9940400-9953600	Weak transcription	Right Atrium	heart
3	chr2:9946000-9953600	Weak transcription	Osteobl	bone
4	chr2:9949800-9954200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:9950000-9953600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:9950000-9953600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:9950000-9953600	Weak transcription	HMEC	breast
8	chr2:9950000-9953800	Weak transcription	Lung	lung
9	chr2:9950000-9953800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:9950000-9953800	Weak transcription	HSMM	muscle
11	chr2:9950200-9953600	Weak transcription	Colonic Mucosa	Colon
12	chr2:9950200-9953600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:9950200-9953800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:9950200-9953800	Weak transcription	Fetal Thymus	thymus
15	chr2:9950200-9953800	Weak transcription	Gastric	stomach
16	chr2:9950400-9953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:9950800-9954800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:9951200-9953600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:9951200-9954800	Enhancers	Esophagus	oesophagus
20	chr2:9951200-9955000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:9951800-9953800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:9951800-9953800	Weak transcription	A549	lung
23	chr2:9951800-9954400	Enhancers	HUVEC	blood vessel
24	chr2:9952000-9954400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:9952200-9955600	Enhancers	Placenta	Placenta
26	chr2:9952400-9953600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:9952400-9954600	Enhancers	K562	blood
28	chr2:9952600-9953600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:9952600-9954200	Weak transcription	Psoas Muscle	Psoas
30	chr2:9952600-9954400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr2:9952600-9954400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:9952800-9953800	Weak transcription	Pancreas	Pancrea
33	chr2:9952800-9954400	Enhancers	Stomach Mucosa	stomach
34	chr2:9952800-9956000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:9953200-9953600	Weak transcription	NHEK	skin
36	chr2:9953200-9954000	Enhancers	Primary hematopoietic stem cells	blood
37	chr2:9953200-9954200	Enhancers	Primary B cells from cord blood	blood
38	chr2:9953200-9954200	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr2:9953200-9954200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:9953400-9953600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:9953400-9953800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:9953400-9954400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:9953400-9954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:9953400-9954400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr2:9953400-9954400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:9953400-9954400	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr2:9953400-9954800	Enhancers	Right Ventricle	heart
48	chr2:9953400-9954800	Enhancers	Spleen	Spleen
49	chr2:9953400-9955000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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