Variant report

Variant	rs12915072
Chromosome Location	chr15:93472582-93472583
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93464070..93466374-chr15:93470199..93472633,2	MCF-7	breast:
2	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:
3	chr15:93471024..93473463-chr15:93480007..93483726,4	MCF-7	breast:
4	chr15:93466975..93470280-chr15:93472259..93475491,4	MCF-7	breast:
5	chr15:93471074..93473914-chr15:93495809..93497722,2	K562	blood:
6	chr15:93446137..93449802-chr15:93471461..93474569,3	K562	blood:
7	chr15:93447864..93450359-chr15:93471723..93473623,2	K562	blood:
8	chr15:93459389..93462852-chr15:93472444..93474181,3	K562	blood:
9	chr15:93459389..93460980-chr15:93471786..93474181,2	K562	blood:
10	chr15:93466503..93469874-chr15:93472083..93475098,4	K562	blood:
11	chr15:93345772..93348684-chr15:93471870..93473819,2	K562	blood:
12	chr15:93445926..93447637-chr15:93471053..93473390,2	K562	blood:
13	chr15:93443271..93444821-chr15:93472288..93474451,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction
ENSG00000264173	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10520717	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10520719	0.81[CEU][hapmap]
rs11074127	0.85[CEU][hapmap]
rs11630582	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs11632522	0.85[AMR][1000 genomes]
rs11634204	0.87[AMR][1000 genomes]
rs11634207	0.81[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11857145	0.82[CEU][hapmap]
rs12901651	1.00[ASN][1000 genomes]
rs12901950	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12904680	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906132	0.81[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs12907579	0.81[CEU][hapmap]
rs12914508	0.83[AMR][1000 genomes]
rs12916015	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1534779	0.81[CEU][hapmap]
rs17525800	0.81[CEU][hapmap]
rs2033844	0.81[CEU][hapmap]
rs2119010	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2272457	0.81[CEU][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs28540863	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28668136	0.87[AMR][1000 genomes]
rs34266454	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34498571	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35327372	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35477598	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35596808	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36048863	0.89[AMR][1000 genomes]
rs3784786	0.81[CEU][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs3817597	0.82[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs4778067	0.80[AMR][1000 genomes]
rs56062215	1.00[ASN][1000 genomes]
rs56358327	0.87[AMR][1000 genomes]
rs57114827	1.00[ASN][1000 genomes]
rs58589040	1.00[ASN][1000 genomes]
rs67190144	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72761955	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12915072	CHD2	Cis_1M	lymphoblastoid	RTeQTL
rs12915072	FAM174B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:93463200-93486800	Strong transcription	Dnd41	blood
6	chr15:93464200-93475000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:93464400-93473600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:93466000-93473000	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr15:93466000-93473600	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:93466000-93476200	Strong transcription	Placenta	Placenta
12	chr15:93466200-93473200	Strong transcription	Hela-S3	cervix
13	chr15:93466200-93475000	Strong transcription	HUVEC	blood vessel
14	chr15:93466200-93477000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:93466200-93479200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:93466200-93480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
19	chr15:93466200-93489400	Strong transcription	K562	blood
20	chr15:93466400-93473200	Strong transcription	NHEK	skin
21	chr15:93466400-93473400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:93466400-93473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:93466400-93475800	Strong transcription	Liver	Liver
24	chr15:93466400-93476400	Weak transcription	Fetal Heart	heart
25	chr15:93466400-93476800	Strong transcription	Primary hematopoietic stem cells	blood
26	chr15:93466400-93480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:93466600-93472600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:93466600-93473200	Weak transcription	Right Atrium	heart
30	chr15:93466600-93474200	Strong transcription	HepG2	liver
31	chr15:93466600-93476400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
33	chr15:93466800-93473200	Strong transcription	HMEC	breast
34	chr15:93466800-93479600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:93467200-93476200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:93467400-93476400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:93467400-93477000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
42	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr15:93467600-93474800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:93467800-93473000	Strong transcription	NHLF	lung
47	chr15:93467800-93473200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:93467800-93478600	Strong transcription	Primary T cells from cord blood	blood
49	chr15:93467800-93480000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:93468000-93473800	Strong transcription	Brain Hippocampus Middle	brain

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