Variant report

Variant	rs12442820
Chromosome Location	chr15:72459440-72459441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72454000..72456435-chr15:72458895..72460767,2	MCF-7	breast:
2	chr15:72458549..72461101-chr15:72765178..72767894,2	K562	blood:
3	chr15:72459257..72462704-chr15:72465780..72468461,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261423	Chromatin interaction
ENSG00000175318	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10220917	1.00[CHB][hapmap]
rs12324592	1.00[CHB][hapmap]
rs12438558	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12438985	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12439301	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12441028	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12441217	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12441866	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12443060	1.00[ASW][hapmap]
rs16956382	1.00[ASN][1000 genomes]
rs16956384	1.00[ASN][1000 genomes]
rs16956391	1.00[ASN][1000 genomes]
rs16956450	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956519	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956759	1.00[CHB][hapmap]
rs16956826	1.00[CHB][hapmap]
rs1842666	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912211	1.00[CHB][hapmap]
rs2912212	1.00[CHB][hapmap]
rs34850275	1.00[ASN][1000 genomes]
rs35886932	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6495002	1.00[CHB][hapmap]
rs8192349	0.83[AMR][1000 genomes]
rs8192419	0.83[AMR][1000 genomes]
rs8192422	0.83[AMR][1000 genomes]
rs9806212	1.00[CHB][hapmap]
rs9806374	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448400-72460800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:72448600-72460800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:72448600-72460800	Weak transcription	Right Atrium	heart
4	chr15:72448800-72459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:72448800-72460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:72449000-72459800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:72449200-72460400	Weak transcription	Fetal Kidney	kidney
9	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:72453000-72459800	Strong transcription	Fetal Intestine Small	intestine
11	chr15:72453000-72460000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:72454600-72460000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:72454600-72460600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:72455200-72460000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:72455200-72460000	Weak transcription	Lung	lung
17	chr15:72455200-72460400	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:72456400-72460400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:72456600-72460000	Weak transcription	Fetal Brain Male	brain
20	chr15:72456600-72460600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:72456600-72460600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:72456600-72461000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:72456800-72460400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:72456800-72460400	Weak transcription	Fetal Brain Female	brain
25	chr15:72457800-72460600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:72457800-72462000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:72458600-72459600	Genic enhancers	Placenta	Placenta
28	chr15:72458600-72463600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr15:72458800-72459600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:72458800-72460600	Enhancers	Fetal Lung	lung
31	chr15:72459200-72459600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:72459200-72459600	Genic enhancers	HMEC	breast
33	chr15:72459200-72460400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr15:72459400-72461400	Enhancers	Fetal Stomach	stomach

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