Variant report

Variant	rs66851469
Chromosome Location	chr15:83479349-83479350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:139)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:139 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr15:83478877-83480275	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:83478181-83479415	HUVEC	blood vessel:	n/a	n/a
3	CEBPB	chr15:83479212-83479564	IMR90	lung:	n/a	n/a
4	POLR2A	chr15:83478084-83479399	MCF-7	breast:	n/a	n/a
5	ELF1	chr15:83479227-83479488	HepG2	liver:	n/a	chr15:83479383-83479394
6	WRNIP1	chr15:83479271-83479468	GM12878	blood:	n/a	n/a
7	MTA3	chr15:83479122-83480316	GM12878	blood:	n/a	n/a
8	SMARCB1	chr15:83478067-83479519	Hela-S3	cervix:	n/a	n/a
9	CHD1	chr15:83478017-83480145	GM12878	blood:	n/a	n/a
10	PAX5	chr15:83479026-83480351	GM12878	blood:	n/a	chr15:83480341-83480351
11	ELK4	chr15:83479101-83479426	Hela-S3	cervix:	n/a	n/a
12	SIN3AK20	chr15:83479129-83479480	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr15:83478062-83479517	ProgFib	skin:	n/a	n/a
14	POLR2A	chr15:83479242-83480206	GM12891	blood:	n/a	n/a
15	POLR2A	chr15:83478115-83479366	MCF-7	breast:	n/a	n/a
16	MAFK	chr15:83479228-83479572	Hela-S3	cervix:	n/a	n/a
17	NFIC	chr15:83479199-83480407	GM12878	blood:	n/a	n/a
18	BCL11A	chr15:83479278-83480283	GM12878	blood:	n/a	n/a
19	MXI1	chr15:83479008-83479888	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:83478016-83479566	PBDE	blood:	n/a	n/a
21	CHD2	chr15:83478023-83479366	HepG2	liver:	n/a	n/a
22	FOXP2	chr15:83478613-83479373	PFSK-1	brain:	n/a	n/a
23	CEBPB	chr15:83479061-83479583	A549	lung:	n/a	n/a
24	ATF2	chr15:83479287-83480364	GM12878	blood:	n/a	n/a
25	CHD2	chr15:83478006-83480145	GM12878	blood:	n/a	n/a
26	IRF4	chr15:83479208-83479810	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:83477963-83479741	GM19099	blood:	n/a	n/a
28	BCLAF1	chr15:83479251-83480322	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:83479180-83479422	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:83477789-83479413	GM18951	blood:	n/a	n/a
31	SIN3A	chr15:83478016-83479545	H1-hESC	embryonic stem cell:	n/a	chr15:83479327-83479340
32	CEBPB	chr15:83479189-83480121	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:83479314-83479556	GM12891	blood:	n/a	n/a
34	ELF1	chr15:83478177-83479431	GM12878	blood:	n/a	chr15:83479383-83479394
35	POLR2A	chr15:83478129-83479379	Gliobla	brain:	n/a	n/a
36	POLR2A	chr15:83479051-83479478	U87	brain:	n/a	n/a
37	TEAD4	chr15:83479113-83479659	HepG2	liver:	n/a	n/a
38	POLR2A	chr15:83478091-83480332	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:83478174-83479401	GM12878	blood:	n/a	n/a
40	SIN3AK20	chr15:83479234-83479460	HepG2	liver:	n/a	n/a
41	TCF12	chr15:83479138-83479471	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr15:83478016-83479409	K562	blood:	n/a	n/a
43	POLR2A	chr15:83478146-83479376	K562	blood:	n/a	n/a
44	HCFC1	chr15:83477536-83480275	Hela-S3	cervix:	n/a	n/a
45	E2F1	chr15:83478352-83479357	Hela-S3	cervix:	n/a	chr15:83479251-83479258 chr15:83479251-83479258 chr15:83478439-83478448 chr15:83479251-83479258
46	UBTF	chr15:83478120-83479904	K562	blood:	n/a	n/a
47	MAFK	chr15:83479260-83480066	IMR90	lung:	n/a	n/a
48	MAX	chr15:83477996-83479353	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:83477951-83480455	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:83477132-83479406	GM12892	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83478234..83479933-chr15:83485060..83487669,2	K562	blood:
2	chr15:83423255..83426158-chr15:83477607..83479598,3	MCF-7	breast:
3	chr15:83478686..83480372-chr15:83679248..83681221,2	MCF-7	breast:
4	chr15:83478452..83480034-chr15:83499455..83501748,2	MCF-7	breast:
5	chr15:83475882..83480852-chr15:83678880..83683242,6	MCF-7	breast:
6	chr15:83376836..83378789-chr15:83478421..83480593,2	MCF-7	breast:
7	chr15:83477828..83481866-chr15:83483118..83489176,7	K562	blood:
8	chr15:83347885..83349520-chr15:83478710..83480628,2	MCF-7	breast:
9	chr15:83313427..83317808-chr15:83477553..83483000,6	K562	blood:
10	chr15:83407361..83409606-chr15:83477408..83479472,2	MCF-7	breast:
11	chr15:83478211..83480402-chr15:83735487..83737469,2	MCF-7	breast:
12	chr15:83417500..83421911-chr15:83474614..83480217,8	MCF-7	breast:
13	chr15:83478559..83480416-chr15:83489248..83490840,2	MCF-7	breast:
14	chr15:83417832..83422548-chr15:83476028..83480956,9	K562	blood:
15	chr15:83479049..83481749-chr15:83503841..83505564,2	K562	blood:
16	chr15:83477527..83479377-chr15:83517237..83519936,2	K562	blood:
17	chr15:83333197..83334998-chr15:83479229..83480988,2	MCF-7	breast:
18	chr15:83476923..83480237-chr15:83875108..83878990,4	MCF-7	breast:
19	chr15:83477632..83480172-chr15:83484528..83487051,2	MCF-7	breast:
20	chr15:83477529..83479377-chr15:83517237..83520056,3	K562	blood:
21	chr15:83477554..83479674-chr15:83486165..83489315,3	MCF-7	breast:
22	chr15:83417361..83424147-chr15:83476165..83481050,26	MCF-7	breast:
23	chr15:83348193..83350766-chr15:83477443..83480779,4	MCF-7	breast:
24	chr15:83417749..83420684-chr15:83476028..83479878,6	K562	blood:

No data

Variant related genes	Relation type
FSD2	TF binding region
ENSG00000259462	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000259315	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000263643	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000252690	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11259948	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11259949	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11259952	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1271044	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12902970	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903411	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12907913	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1971555	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379996	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2890314	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025432	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8041231	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	esv3371602	chr15:83476798-83481096	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
5	esv3334500	chr15:83478048-83480146	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66851469	WHAMM	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83477400-83480400	Active TSS	Colonic Mucosa	Colon
2	chr15:83477400-83480400	Active TSS	Stomach Mucosa	stomach
3	chr15:83477400-83481000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:83477600-83479600	Active TSS	Brain Anterior Caudate	brain
5	chr15:83477600-83480200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr15:83477600-83480400	Active TSS	Psoas Muscle	Psoas
7	chr15:83477600-83480800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:83477800-83479400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:83477800-83479400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:83477800-83479400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr15:83477800-83479400	Active TSS	HepG2	liver
12	chr15:83477800-83479600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr15:83477800-83479600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:83477800-83479600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr15:83477800-83479800	Active TSS	Fetal Brain Male	brain
16	chr15:83477800-83480000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:83477800-83480000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:83477800-83480200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:83477800-83480400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr15:83477800-83480400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr15:83477800-83481000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:83478000-83479400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:83478000-83479400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:83478000-83479400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:83478000-83479600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:83478000-83479800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:83478000-83479800	Active TSS	Brain Hippocampus Middle	brain
28	chr15:83478000-83479800	Active TSS	Small Intestine	intestine
29	chr15:83478000-83480200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr15:83478000-83480200	Active TSS	Fetal Muscle Trunk	muscle
31	chr15:83478000-83480200	Active TSS	Placenta	Placenta
32	chr15:83478000-83480400	Active TSS	Aorta	Aorta
33	chr15:83478000-83480400	Active TSS	Fetal Intestine Small	intestine
34	chr15:83478000-83480400	Active TSS	Fetal Kidney	kidney
35	chr15:83478000-83480400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr15:83478000-83480400	Active TSS	Ovary	ovary
37	chr15:83478000-83480400	Active TSS	Right Ventricle	heart
38	chr15:83478000-83480400	Active TSS	Stomach Smooth Muscle	stomach
39	chr15:83478000-83480600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:83478000-83480800	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr15:83478000-83480800	Active TSS	NH-A	brain
42	chr15:83478000-83481000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:83478000-83481400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr15:83478200-83479400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:83478200-83479400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr15:83478200-83479400	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:83478200-83479400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:83478200-83479400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:83478200-83479400	Active TSS	Liver	Liver
50	chr15:83478200-83479400	Active TSS	Brain Cingulate Gyrus	brain

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