Variant report

Variant	rs12906626
Chromosome Location	chr15:83680426-83680427
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:667)
CpG islands
(count:61)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:667 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr15:83679368-83680879	K562	blood:	n/a	n/a
2	ARID3A	chr15:83680271-83680471	HepG2	liver:	n/a	n/a
3	RAD21	chr15:83680204-83680632	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:83680338-83680594	GM10266	blood:	n/a	n/a
5	GTF2F1	chr15:83680197-83681061	K562	blood:	n/a	n/a
6	GABPA	chr15:83680217-83680610	H1-hESC	embryonic stem cell:	n/a	chr15:83680388-83680402 chr15:83680391-83680402 chr15:83680393-83680402 chr15:83680391-83680405
7	GABPA	chr15:83679631-83680897	A549	lung:	n/a	chr15:83680388-83680402 chr15:83680391-83680402 chr15:83680393-83680402 chr15:83680391-83680405
8	MAX	chr15:83679626-83680949	MCF-7	breast:	n/a	n/a
9	RAD21	chr15:83680291-83680692	Hela-S3	cervix:	n/a	n/a
10	CEBPD	chr15:83680180-83680691	K562	blood:	n/a	n/a
11	BCL3	chr15:83680095-83681014	A549	lung:	n/a	n/a
12	CTCF	chr15:83680420-83680570	NHLF	lung:	n/a	n/a
13	CTCF	chr15:83680305-83680646	GM19238	blood:	n/a	n/a
14	STAT1	chr15:83680137-83680936	GM12878	blood:	n/a	chr15:83680646-83680660
15	YY1	chr15:83679558-83680673	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr15:83678960-83682105	GM12891	blood:	n/a	n/a
17	STAT5A	chr15:83680248-83680801	K562	blood:	n/a	chr15:83680646-83680660
18	E2F4	chr15:83680141-83680806	K562	blood:	n/a	chr15:83680392-83680401
19	CTCF	chr15:83680320-83680470	HAc	cerebellar:	n/a	n/a
20	CBX3	chr15:83680286-83681010	K562	blood:	n/a	n/a
21	POLR2A	chr15:83679681-83680799	ProgFib	skin:	n/a	n/a
22	SP2	chr15:83680223-83680572	K562	blood:	n/a	n/a
23	POLR2A	chr15:83679662-83680819	NB4	blood:	n/a	n/a
24	CTCF	chr15:83680340-83680490	NHEK	skin:	n/a	n/a
25	MAX	chr15:83679584-83680980	GM12878	blood:	n/a	n/a
26	ZNF143	chr15:83679590-83680657	H1-hESC	embryonic stem cell:	n/a	chr15:83680423-83680433
27	CTCF	chr15:83680215-83680667	T-47D	breast:	n/a	n/a
28	CTCF	chr15:83680380-83680530	GM12878	blood:	n/a	n/a
29	RELA	chr15:83679597-83681036	GM18951	blood:	n/a	n/a
30	SMC3	chr15:83680259-83680808	K562	blood:	n/a	n/a
31	POLR2A	chr15:83679488-83681032	HUVEC	blood vessel:	n/a	n/a
32	SIN3AK20	chr15:83679488-83680870	A549	lung:	n/a	n/a
33	CTCF	chr15:83680263-83680600	K562	blood:	n/a	n/a
34	CTCF	chr15:83680351-83680575	GM20000	blood:	n/a	n/a
35	RAD21	chr15:83679419-83680715	IMR90	lung:	n/a	n/a
36	TAF1	chr15:83680100-83680818	K562	blood:	n/a	n/a
37	RCOR1	chr15:83680256-83680983	GM12878	blood:	n/a	n/a
38	RCOR1	chr15:83679627-83680777	HepG2	liver:	n/a	n/a
39	TCF7L2	chr15:83680161-83680805	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr15:83679762-83680935	GM12892	blood:	n/a	n/a
41	CTCF	chr15:83680354-83680582	GM13976	blood:	n/a	n/a
42	SP2	chr15:83680097-83680697	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:83679685-83680870	GM12878	blood:	n/a	n/a
44	TBP	chr15:83680223-83680692	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr15:83679581-83680809	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr15:83679670-83680946	GM12891	blood:	n/a	n/a
47	SMC3	chr15:83679550-83680906	GM12878	blood:	n/a	n/a
48	MYC	chr15:83679606-83680733	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr15:83679525-83681003	PFSK-1	brain:	n/a	n/a
50	CTCF	chr15:83679502-83680761	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:83680418-83680468	GM19239	blood:	n/a
2	chr15:83680418-83680468	HPAEpiC	pulmonary alveolar:	n/a
3	chr15:83680418-83680468	HCPEpiC	choroid plexus:	n/a
4	chr15:83680418-83680468	HepG2	liver:	n/a
5	chr15:83680418-83680468	T-47D	breast:	n/a
6	chr15:83680418-83680468	RPTEC	kidney:	n/a
7	chr15:83680418-83680468	PANC-1	pancreas:	n/a
8	chr15:83680418-83680468	MCF-7	breast:	n/a
9	chr15:83680418-83680468	AG09309	skin:	n/a
10	chr15:83680418-83680468	HIPEpiC	eye:	n/a
11	chr15:83680418-83680468	AG09319	gingival:	n/a
12	chr15:83680418-83680468	NT2-D1	testis:	n/a
13	chr15:83680418-83680468	HCF	heart:	n/a
14	chr15:83680418-83680468	SK-N-MC	brain:	n/a
15	chr15:83680418-83680468	SAEC	small airway:	n/a
16	chr15:83680418-83680468	ovcar-3	ovarian:	n/a
17	chr15:83680418-83680468	NHDF-neo	bronchial:	n/a
18	chr15:83680418-83680468	HL-60	blood:	n/a
19	chr15:83680418-83680468	HNPCEpiC	eye:	n/a
20	chr15:83680418-83680468	K562	blood:	n/a
21	chr15:83680418-83680468	NH-A	brain:	n/a
22	chr15:83680418-83680468	CMK	blood:	n/a
23	chr15:83680418-83680468	SK-N-SH_RA	brain:	n/a
24	chr15:83680418-83680468	GM06990	blood:	n/a
25	chr15:83680418-83680468	Jurkat	blood:	n/a
26	chr15:83680418-83680468	SKMC	muscle:	n/a
27	chr15:83680418-83680468	PrEC	prostate:	n/a
28	chr15:83680418-83680468	Hepatocyte	liver:	n/a
29	chr15:83680418-83680468	HMEC	breast:	n/a
30	chr15:83680418-83680468	HRE	kidney:	n/a
31	chr15:83680418-83680468	NB4	blood:	n/a
32	chr15:83680418-83680468	AG10803	skin:	n/a
33	chr15:83680418-83680468	NHBE	bronchial:	n/a
34	chr15:83680418-83680468	HRPEpiC	eye:	n/a
35	chr15:83680418-83680468	HAEpiC	amniotic membrane:	n/a
36	chr15:83680418-83680468	GM12878	blood:	n/a
37	chr15:83680418-83680468	ProgFib	skin:	n/a
38	chr15:83680418-83680468	GM12891	blood:	n/a
39	chr15:83680418-83680468	Hela-S3	cervix:	n/a
40	chr15:83680418-83680468	MCF10A-Er-Src	breast:	n/a
41	chr15:83680418-83680468	AoSMC	blood vessel:	n/a
42	chr15:83680418-83680468	SK-N-SH	brain:	n/a
43	chr15:83680418-83680468	IMR90	lung:	fetal
44	chr15:83680418-83680468	HRCEpiC	kidney:	n/a
45	chr15:83680418-83680468	ECC-1	luminal epithelium:	n/a
46	chr15:83680418-83680468	PFSK-1	brain:	n/a
47	chr15:83680418-83680468	U87	brain:	n/a
48	chr15:83680418-83680468	AG04450	lung:	fetal
49	chr15:83680418-83680468	GM12892	blood:	n/a
50	chr15:83680418-83680468	H1-hESC	embryonic stem cell:	embryo

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83678535..83684480-chr15:83731660..83738533,12	MCF-7	breast:
2	chr15:83516928..83520058-chr15:83678480..83682741,4	K562	blood:
3	chr15:83679004..83681789-chr15:83733343..83738150,8	MCF-7	breast:
4	chr15:83348285..83351278-chr15:83678934..83682211,3	MCF-7	breast:
5	chr15:83679195..83681271-chr15:83795082..83797349,2	K562	blood:
6	chr15:83418143..83420234-chr15:83679510..83682009,2	K562	blood:
7	chr15:83678614..83685168-chr15:83874398..83879059,12	MCF-7	breast:
8	chr15:83679523..83682277-chr15:83776010..83777597,2	K562	blood:
9	chr15:83417632..83419477-chr15:83677725..83680505,2	MCF-7	breast:
10	chr15:83679205..83686226-chr15:83733349..83739878,12	K562	blood:
11	chr15:83654223..83656996-chr15:83678905..83681492,4	MCF-7	breast:
12	chr15:83679499..83683217-chr15:83687466..83692124,6	K562	blood:
13	chr14:34419671..34420196-chr15:83680007..83680593,2	Hela-S3	cervix:
14	chr15:83314747..83316448-chr15:83680031..83681739,2	K562	blood:
15	chr15:83678350..83680791-chr15:83692946..83695679,3	MCF-7	breast:
16	chr15:83678946..83682301-chr15:83733959..83737732,7	K562	blood:
17	chr15:83678260..83683197-chr15:83874959..83878158,5	K562	blood:
18	chr15:83678154..83684518-chr15:83871554..83879371,12	MCF-7	breast:
19	chr15:83679404..83681095-chr21:46492672..46494798,2	MCF-7	breast:
20	chr15:83475882..83480852-chr15:83678880..83683242,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260608	TF binding region
ENSG00000249214	TF binding region
C15orf40	TF binding region
ENSG00000260608	CpG island
C15orf40	CpG island
ENSG00000249214	CpG island
ENSG00000235374	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000129521	Chromatin interaction
ENSG00000169612	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000259767	Chromatin interaction
ENSG00000136404	Chromatin interaction
ENSG00000260351	Chromatin interaction
ENSG00000103942	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000263643	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10400812	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858074	0.95[ASN][1000 genomes]
rs12439782	0.85[EUR][1000 genomes]
rs12592391	0.95[ASN][1000 genomes]
rs12593316	0.82[ASN][1000 genomes]
rs12899522	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900411	0.95[ASN][1000 genomes]
rs12901811	0.95[ASN][1000 genomes]
rs12902721	0.89[ASN][1000 genomes]
rs12903066	0.95[ASN][1000 genomes]
rs12904695	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906027	0.95[ASN][1000 genomes]
rs12907032	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911706	0.95[ASN][1000 genomes]
rs12911891	0.95[ASN][1000 genomes]
rs12913130	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917594	0.94[ASN][1000 genomes]
rs13329195	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329269	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17158127	0.95[ASN][1000 genomes]
rs17507300	0.98[ASN][1000 genomes]
rs2084839	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2381030	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485801	0.97[ASN][1000 genomes]
rs28580677	0.97[ASN][1000 genomes]
rs3087804	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869943	0.92[ASN][1000 genomes]
rs35207081	0.95[ASN][1000 genomes]
rs35627116	0.94[ASN][1000 genomes]
rs36038412	0.95[ASN][1000 genomes]
rs4079029	0.97[ASN][1000 genomes]
rs61375537	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6603044	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603046	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66606849	0.95[ASN][1000 genomes]
rs67482297	0.95[ASN][1000 genomes]
rs67822554	0.95[ASN][1000 genomes]
rs7163516	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166645	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170547	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172665	0.89[EUR][1000 genomes]
rs7177599	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181169	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750214	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757	0.95[ASN][1000 genomes]
rs8031896	0.98[ASN][1000 genomes]
rs8040457	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040998	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646239	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12906626	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs12906626	BTBD1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83679000-83680600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr15:83679000-83680800	Active TSS	A549	lung
3	chr15:83679200-83680600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:83679200-83680600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:83679200-83680600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:83679200-83681400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:83679200-83681400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:83679400-83680600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:83679400-83680600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:83679400-83680600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:83679400-83680600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:83679400-83680600	Active TSS	GM12878-XiMat	blood
13	chr15:83679400-83680600	Active TSS	HSMM	muscle
14	chr15:83679400-83680800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr15:83679400-83680800	Active TSS	Aorta	Aorta
16	chr15:83679400-83680800	Active TSS	Right Ventricle	heart
17	chr15:83679400-83681000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:83679400-83681000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:83679400-83681000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr15:83679400-83681200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr15:83679400-83681200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr15:83679400-83681400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:83679600-83680600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:83679600-83680600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:83679600-83680600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:83679600-83680600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:83679600-83680600	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr15:83679600-83680600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:83679600-83680600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:83679600-83680600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:83679600-83680600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:83679600-83680600	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:83679600-83680600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:83679600-83680600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:83679600-83680600	Active TSS	Brain Hippocampus Middle	brain
36	chr15:83679600-83680600	Active TSS	Colon Smooth Muscle	Colon
37	chr15:83679600-83680600	Active TSS	Esophagus	oesophagus
38	chr15:83679600-83680600	Active TSS	Fetal Brain Female	brain
39	chr15:83679600-83680600	Active TSS	Fetal Heart	heart
40	chr15:83679600-83680600	Active TSS	Fetal Intestine Large	intestine
41	chr15:83679600-83680600	Active TSS	Lung	lung
42	chr15:83679600-83680600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr15:83679600-83680600	Active TSS	Rectal Smooth Muscle	rectum
44	chr15:83679600-83680600	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr15:83679600-83680600	Active TSS	Dnd41	blood
46	chr15:83679600-83680600	Active TSS	HMEC	breast
47	chr15:83679600-83680600	Active TSS	HSMMtube	muscle
48	chr15:83679600-83680600	Active TSS	K562	blood
49	chr15:83679600-83680600	Active TSS	NHDF-Ad	bronchial
50	chr15:83679600-83680600	Active TSS	NHLF	lung

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