Variant report

Variant	rs3935339
Chromosome Location	chr15:77322029-77322030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:77321962-77322070	Pancreas_OC	pancreas:	n/a	n/a
2	CTCF	chr15:77321940-77322090	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr15:77321936-77322069	K562	blood:	n/a	n/a
4	RAD21	chr15:77321899-77322066	K562	blood:	n/a	n/a
5	POLR2A	chr15:77320435-77330647	HL-60	blood:	n/a	n/a
6	POLR2A	chr15:77321667-77330508	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr15:77321956-77322064	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr15:77321880-77322030	K562	blood:	n/a	n/a
9	CTCF	chr15:77321845-77322106	K562	blood:	n/a	n/a
10	CTCF	chr15:77321980-77322130	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr15:77321958-77322088	K562	blood:	n/a	n/a
12	CTCF	chr15:77321964-77322057	MCF-7	breast:	n/a	n/a
13	CTCF	chr15:77321959-77322057	MCF-7	breast:	n/a	n/a
14	CTCF	chr15:77321920-77322070	A549	lung:	n/a	n/a
15	RAD21	chr15:77321916-77322071	HepG2	liver:	n/a	n/a
16	CTCF	chr15:77321952-77322089	NHEK	skin:	n/a	n/a
17	CTCF	chr15:77321920-77322070	HepG2	liver:	n/a	n/a
18	MAZ	chr15:77321880-77322099	HepG2	liver:	n/a	n/a
19	UBTF	chr15:77321839-77322039	K562	blood:	n/a	n/a
20	CTCF	chr15:77322000-77322150	NHEK	skin:	n/a	n/a
21	CTCF	chr15:77321965-77322053	HepG2	liver:	n/a	n/a
22	SMC3	chr15:77321982-77322053	HepG2	liver:	n/a	n/a
23	CTCF	chr15:77321757-77322209	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77320466..77323005-chr15:77324460..77327682,3	MCF-7	breast:
2	chr15:77320639..77324428-chr15:77362244..77364696,3	K562	blood:

No data

Variant related genes	Relation type
PSTPIP1	TF binding region
ENSG00000140368	Chromatin interaction
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11630497	0.86[JPT][hapmap]
rs11636613	0.87[JPT][hapmap]
rs11737	0.87[JPT][hapmap]
rs12372961	0.87[JPT][hapmap]
rs12903227	0.83[CHB][hapmap]
rs16968665	0.82[JPT][hapmap]
rs2404233	0.87[JPT][hapmap]
rs2404234	0.87[JPT][hapmap]
rs4078354	0.83[CHB][hapmap]
rs4886509	0.87[JPT][hapmap]
rs4886847	0.87[JPT][hapmap]
rs56103874	0.84[AFR][1000 genomes]
rs8032	0.87[JPT][hapmap]
rs938501	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1808532	chr15:77257714-77332539	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1035874	chr15:77266776-77328742	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1822592	chr15:77283956-77332539	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv570111	chr15:77286693-77332606	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv1048833	chr15:77294593-77339260	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv1848501	chr15:77301357-77327571	Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1804890	chr15:77302969-77332482	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1836749	chr15:77302969-77332606	Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1842687	chr15:77307260-77332606	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935339	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77307400-77322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:77308800-77327600	Weak transcription	Esophagus	oesophagus
3	chr15:77312200-77328400	Weak transcription	Aorta	Aorta
4	chr15:77313000-77327800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:77313400-77327200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr15:77314600-77328000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:77314800-77330000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:77315000-77322800	Weak transcription	HSMMtube	muscle
9	chr15:77315000-77323400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:77315400-77322600	Weak transcription	HSMM	muscle
11	chr15:77315400-77323200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:77315400-77330400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:77315400-77330600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr15:77316600-77323200	Weak transcription	Fetal Thymus	thymus
15	chr15:77316800-77322600	Weak transcription	A549	lung
16	chr15:77316800-77322800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:77316800-77323400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:77316800-77323400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:77316800-77327000	Weak transcription	Brain Substantia Nigra	brain
20	chr15:77316800-77327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:77316800-77327800	Weak transcription	GM12878-XiMat	blood
22	chr15:77316800-77330200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:77317400-77326200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:77317400-77329800	Strong transcription	Primary T cells from cord blood	blood
25	chr15:77317400-77330600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:77317600-77323400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:77317600-77330400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:77317800-77322400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:77318400-77350600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:77319400-77322800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:77319600-77322400	Strong transcription	Thymus	Thymus
32	chr15:77319600-77322600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:77319600-77327200	Weak transcription	Brain Angular Gyrus	brain
34	chr15:77320000-77322600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:77320000-77322600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr15:77320000-77323200	Weak transcription	Primary B cells from cord blood	blood
37	chr15:77320600-77323600	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr15:77320600-77325800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:77320800-77323000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr15:77320800-77325200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:77321000-77322400	Weak transcription	Brain Anterior Caudate	brain
42	chr15:77321000-77322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:77321000-77322800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:77321000-77322800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:77321000-77323000	Enhancers	Duodenum Mucosa	Duodenum
46	chr15:77321000-77323200	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:77321000-77323200	Bivalent Enhancer	Fetal Intestine Large	intestine
48	chr15:77321000-77323200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr15:77321000-77325600	Weak transcription	Right Atrium	heart
50	chr15:77321000-77328200	Weak transcription	H9 Cell Line	embryonic stem cell

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