Variant report

Variant	rs12901651
Chromosome Location	chr15:93445783-93445784
allele	A/G
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	chr15:93442973-93453321	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:93433692-93455675	K562	blood:	n/a	n/a
3	POLR2A	chr15:93445723-93452019	IMR90	lung:	n/a	n/a
4	POLR2A	chr15:93443026-93448707	PFSK-1	brain:	n/a	n/a
5	ARID3A	chr15:93445678-93448097	K562	blood:	n/a	n/a
6	POLR2A	chr15:93443087-93448872	MCF-7	breast:	n/a	n/a
7	CHD1	chr15:93443269-93448419	H1-hESC	embryonic stem cell:	n/a	chr15:93447634-93447644 chr15:93448003-93448013
8	POLR2A	chr15:93445764-93446749	K562	blood:	n/a	n/a
9	POLR2A	chr15:93442438-93449413	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:93445726-93448992	GM12878	blood:	n/a	n/a
11	MXI1	chr15:93442841-93449632	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:93445759-93449645	U87	brain:	n/a	n/a
13	POLR2A	chr15:93445782-93450636	MCF10A-Er-Src	breast:	n/a	n/a
14	CHD1	chr15:93442849-93450583	GM12878	blood:	n/a	chr15:93447634-93447644 chr15:93448003-93448013
15	JUN	chr15:93445758-93446793	K562	blood:	n/a	chr15:93446393-93446406 chr15:93446400-93446409 chr15:93446394-93446403
16	POLR2A	chr15:93445753-93449126	MCF10A-Er-Src	breast:	n/a	n/a
17	TBP	chr15:93445772-93448842	Hela-S3	cervix:	n/a	n/a
18	REST	chr15:93442464-93448517	H1-neurons	neurons:	n/a	chr15:93447708-93447721 chr15:93444271-93444291
19	RFX5	chr15:93445667-93449108	SK-N-SH	brain:	n/a	chr15:93447544-93447553 chr15:93447559-93447574
20	POLR2A	chr15:93444832-93448675	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr15:93441953-93448610	Hela-S3	cervix:	n/a	n/a
22	IRF1	chr15:93445742-93450846	K562	blood:	n/a	chr15:93447265-93447279 chr15:93450726-93450735 chr15:93447970-93447984 chr15:93450727-93450736 chr15:93447545-93447554 chr15:93447632-93447646 chr15:93448001-93448015 chr15:93448087-93448100 chr15:93446787-93446799 chr15:93449105-93449119
23	HCFC1	chr15:93445134-93451989	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr15:93445691-93448729	H1-hESC	embryonic stem cell:	n/a	n/a
25	TBL1XR1	chr15:93442055-93449323	K562	blood:	n/a	n/a
26	CHD1	chr15:93442192-93453134	IMR90	lung:	n/a	chr15:93447634-93447644 chr15:93448003-93448013 chr15:93442831-93442841
27	POLR2A	chr15:93445775-93448997	GM18951	blood:	n/a	n/a
28	RFX5	chr15:93445706-93448117	K562	blood:	n/a	chr15:93447544-93447553 chr15:93447559-93447574
29	RFX5	chr15:93445708-93448606	IMR90	lung:	n/a	chr15:93447544-93447553 chr15:93447559-93447574

No.	Distal block	Cell Line	Cell type
1	chr15:93377060..93379186-chr15:93444151..93447492,3	K562	blood:
2	chr15:93393520..93395102-chr15:93444710..93447228,2	K562	blood:
3	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
4	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
5	chr15:93338780..93342194-chr15:93442202..93446226,4	MCF-7	breast:
6	chr11:62537284..62539556-chr15:93444040..93446398,2	MCF-7	breast:
7	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
8	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:

Variant related genes	Relation type
CHD2	TF binding region
MIR3175	TF binding region
ENSG00000267811	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000162227	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12915072	1.00[ASN][1000 genomes]
rs34918115	0.83[AFR][1000 genomes]
rs35327372	1.00[ASN][1000 genomes]
rs56062215	1.00[ASN][1000 genomes]
rs57114827	1.00[ASN][1000 genomes]
rs58589040	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv1851305	chr15:93429646-93446869	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	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
10	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12901651	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93438200-93447200	Weak transcription	Spleen	Spleen
2	chr15:93442600-93446400	Active TSS	Fetal Brain Female	brain
3	chr15:93442600-93449000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:93442800-93446200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:93443000-93445800	Active TSS	Brain Hippocampus Middle	brain
6	chr15:93443000-93445800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr15:93443000-93446200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:93443000-93446400	Active TSS	Stomach Smooth Muscle	stomach
9	chr15:93443000-93448200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:93443000-93448200	Active TSS	NHEK	skin
11	chr15:93443000-93448600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:93443200-93445800	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr15:93443200-93445800	Active TSS	Brain Angular Gyrus	brain
14	chr15:93443200-93445800	Active TSS	Brain Anterior Caudate	brain
15	chr15:93443200-93445800	Active TSS	Brain Cingulate Gyrus	brain
16	chr15:93443200-93445800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr15:93443200-93446000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr15:93443200-93446000	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr15:93443200-93446000	Active TSS	NH-A	brain
20	chr15:93443200-93446200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:93443200-93446400	Active TSS	NHLF	lung
22	chr15:93443200-93446800	Active TSS	HSMMtube	muscle
23	chr15:93443200-93447200	Active TSS	HMEC	breast
24	chr15:93443200-93448000	Active TSS	Brain Substantia Nigra	brain
25	chr15:93443200-93448200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr15:93443200-93448200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr15:93443200-93448200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr15:93443200-93448200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:93443200-93448200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:93443200-93448200	Active TSS	Duodenum Mucosa	Duodenum
31	chr15:93443200-93448400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr15:93443200-93448400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:93443200-93448400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:93443200-93448400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:93443200-93448400	Active TSS	Brain Germinal Matrix	brain
36	chr15:93443200-93448400	Active TSS	Placenta	Placenta
37	chr15:93443200-93448400	Active TSS	Fetal Stomach	stomach
38	chr15:93443200-93448400	Active TSS	HSMM	muscle
39	chr15:93443200-93448600	Active TSS	Colonic Mucosa	Colon
40	chr15:93443200-93448800	Active TSS	Aorta	Aorta
41	chr15:93443200-93448800	Active TSS	Fetal Muscle Trunk	muscle
42	chr15:93443200-93448800	Active TSS	Ovary	ovary
43	chr15:93443200-93449200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:93443200-93449400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:93443200-93449800	Active TSS	Right Ventricle	heart
46	chr15:93443200-93450000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr15:93443200-93450000	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr15:93443400-93445800	Active TSS	Liver	Liver
49	chr15:93443400-93445800	Active TSS	Colon Smooth Muscle	Colon
50	chr15:93443400-93445800	Active TSS	Fetal Intestine Small	intestine

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