Variant report

Variant	rs35270670
Chromosome Location	chr15:83481880-83481881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83481184-83482387	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:83481705-83482086	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:83481869-83481919	HepG2	liver:	n/a
2	chr15:83481869-83481919	SK-N-SH_RA	brain:	n/a
3	chr15:83481869-83481919	GM12892	blood:	n/a
4	chr15:83481869-83481919	HCPEpiC	choroid plexus:	n/a
5	chr15:83481869-83481919	Hepatocyte	liver:	n/a
6	chr15:83481869-83481919	HEEpiC	esophagus:	n/a
7	chr15:83481869-83481919	HRE	kidney:	n/a
8	chr15:83481869-83481919	NT2-D1	testis:	n/a
9	chr15:83481869-83481919	RPTEC	kidney:	n/a
10	chr15:83481869-83481919	HRCEpiC	kidney:	n/a
11	chr15:83481869-83481919	K562	blood:	n/a
12	chr15:83481869-83481919	GM06990	blood:	n/a
13	chr15:83481869-83481919	CMK	blood:	n/a
14	chr15:83481869-83481919	HPAEpiC	pulmonary alveolar:	n/a
15	chr15:83481869-83481919	GM12891	blood:	n/a
16	chr15:83481869-83481919	BJ	skin:	n/a
17	chr15:83481869-83481919	HMEC	breast:	n/a
18	chr15:83481869-83481919	IMR90	lung:	fetal
19	chr15:83481869-83481919	A549	lung:	n/a
20	chr15:83481869-83481919	PrEC	prostate:	n/a
21	chr15:83481869-83481919	NHBE	bronchial:	n/a
22	chr15:83481869-83481919	SK-N-SH	brain:	n/a
23	chr15:83481869-83481919	NH-A	brain:	n/a
24	chr15:83481869-83481919	GM19239	blood:	n/a
25	chr15:83481869-83481919	Jurkat	blood:	n/a
26	chr15:83481869-83481919	AoSMC	blood vessel:	n/a
27	chr15:83481869-83481919	AG09319	gingival:	n/a
28	chr15:83481869-83481919	MCF10A-Er-Src	breast:	n/a
29	chr15:83481869-83481919	SKMC	muscle:	n/a
30	chr15:83481869-83481919	BE2_C	brain:	n/a
31	chr15:83481869-83481919	AG09309	skin:	n/a
32	chr15:83481869-83481919	HEK293	kidney:	embryo
33	chr15:83481869-83481919	LNCaP	prostate:	n/a
34	chr15:83481869-83481919	ECC-1	luminal epithelium:	n/a
35	chr15:83481869-83481919	PFSK-1	brain:	n/a
36	chr15:83481869-83481919	AG04449	skin:	fetal
37	chr15:83481869-83481919	HUVEC	blood vessel:	n/a
38	chr15:83481869-83481919	U87	brain:	n/a
39	chr15:83481869-83481919	NB4	blood:	n/a
40	chr15:83481869-83481919	HCM	heart:	n/a
41	chr15:83481869-83481919	T-47D	breast:	n/a
42	chr15:83481869-83481919	HL-60	blood:	n/a
43	chr15:83481869-83481919	HCF	heart:	n/a
44	chr15:83481869-83481919	PANC-1	pancreas:	n/a
45	chr15:83481869-83481919	HCT-116	colon:	n/a
46	chr15:83481869-83481919	ovcar-3	ovarian:	n/a
47	chr15:83481869-83481919	HRPEpiC	eye:	n/a
48	chr15:83481869-83481919	MCF-7	breast:	n/a
49	chr15:83481869-83481919	HNPCEpiC	eye:	n/a
50	chr15:83481869-83481919	GM12878	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83480184..83483063-chr15:83673551..83675141,2	K562	blood:
2	chr15:83476157..83479071-chr15:83480775..83482878,2	K562	blood:
3	chr15:83481406..83484295-chr15:83488515..83491028,2	MCF-7	breast:
4	chr15:83313427..83317808-chr15:83477553..83483000,6	K562	blood:

No data

Variant related genes	Relation type
WHAMM	TF binding region
WHAMM	CpG island
ENSG00000156232	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000259462	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12899020	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12915294	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35946485	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36111056	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4617830	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7178859	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[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	nsv977747	chr15:83479370-83496161	Weak transcription Active TSS Enhancers Strong transcription Flanking 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	14 gene(s)	inside rSNPs	diseases
5	nsv9288	chr15:83479484-83496828	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35270670	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs35270670	AP3B2	cis	lung	GTEx
rs35270670	AP3B2	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479400-83482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:83479600-83485800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:83479800-83483200	Weak transcription	Gastric	stomach
5	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:83480000-83482000	Weak transcription	Lung	lung
7	chr15:83480000-83482800	Weak transcription	Fetal Brain Female	brain
8	chr15:83480000-83485600	Weak transcription	Esophagus	oesophagus
9	chr15:83480000-83497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:83480200-83484000	Weak transcription	Fetal Brain Male	brain
12	chr15:83480200-83485400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:83480200-83487400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:83480200-83489000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:83480400-83482000	Weak transcription	Fetal Intestine Small	intestine
16	chr15:83480400-83482200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:83480400-83482400	Weak transcription	Fetal Stomach	stomach
18	chr15:83480400-83482400	Weak transcription	HSMM	muscle
19	chr15:83480400-83482600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:83480400-83482800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:83480400-83484000	Weak transcription	Colonic Mucosa	Colon
22	chr15:83480400-83484200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:83480400-83484600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:83480400-83485400	Weak transcription	Thymus	Thymus
25	chr15:83480400-83485800	Weak transcription	Aorta	Aorta
26	chr15:83480400-83487400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:83480400-83488400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:83480400-83493600	Weak transcription	Brain Germinal Matrix	brain
29	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
30	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:83480600-83482600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:83480800-83482000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:83481000-83482000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:83481000-83482000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:83481000-83482000	Enhancers	Primary hematopoietic stem cells	blood
36	chr15:83481000-83482000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr15:83481000-83482000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr15:83481000-83482000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:83481000-83482000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr15:83481000-83482000	Weak transcription	A549	lung
41	chr15:83481000-83482200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr15:83481000-83482400	Weak transcription	Brain Anterior Caudate	brain
43	chr15:83481000-83482400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:83481000-83482400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:83481000-83482400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr15:83481000-83482400	Weak transcription	HMEC	breast
47	chr15:83481000-83482400	Weak transcription	NHEK	skin
48	chr15:83481000-83482600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:83481000-83482600	Weak transcription	Fetal Lung	lung
50	chr15:83481000-83482800	Weak transcription	Brain Angular Gyrus	brain

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