Variant report

Variant	rs13238899
Chromosome Location	chr7:56140618-56140619
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
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	chr7:56140344-56140664	K562	blood:	n/a	n/a
2	POLR2A	chr7:56140513-56143098	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56119174..56121015-chr7:56139907..56143557,3	MCF-7	breast:
2	chr7:56139442..56142282-chr7:56145954..56148779,2	MCF-7	breast:
3	chr7:56140520..56143096-chr7:56151808..56154646,2	K562	blood:
4	chr7:56031348..56032996-chr7:56140272..56142339,2	K562	blood:
5	chr7:56139457..56142087-chr7:56158811..56160685,2	MCF-7	breast:

No data

Variant related genes	Relation type
SUMF2	TF binding region
ENSG00000164776	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs13223226	0.88[EUR][1000 genomes]
rs13226516	0.83[LWK][hapmap]
rs13226699	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13238152	0.84[CHD][hapmap]
rs13238521	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34057777	0.81[CHD][hapmap]
rs34822782	0.97[MKK][hapmap];1.00[YRI][hapmap]
rs35046650	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35210477	0.84[CHD][hapmap]
rs35347055	1.00[YRI][hapmap]
rs35881493	0.97[MKK][hapmap];1.00[YRI][hapmap]
rs3735066	0.84[CHD][hapmap]

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	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13238899	PSPHP1	cis	lung	GTEx
rs13238899	SUMF2	cis	multi-tissue	Pritchard
rs13238899	SUMF2	cis	lymphoblastoid	seeQTL
rs13238899	PSPH	Cis_1M	lymphoblastoid	RTeQTL
rs13238899	SUMF2	cis	Lymphoblastoid	GTEx
rs13238899	PSPHP1	cis	Adipose Subcutaneous	GTEx
rs13238899	ENSG00000129103	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56132400-56141800	Weak transcription	Stomach Mucosa	stomach
3	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
4	chr7:56133200-56141800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:56133200-56141800	Weak transcription	HepG2	liver
6	chr7:56133200-56142000	Weak transcription	Esophagus	oesophagus
7	chr7:56133200-56142200	Weak transcription	Right Atrium	heart
8	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
11	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
12	chr7:56133400-56144200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:56133600-56141800	Weak transcription	HUVEC	blood vessel
15	chr7:56133600-56144200	Weak transcription	NHDF-Ad	bronchial
16	chr7:56133600-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:56133800-56141800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:56133800-56142000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:56133800-56143200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:56134000-56141800	Weak transcription	NHLF	lung
21	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
24	chr7:56134600-56141200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:56134800-56141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:56135000-56141600	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:56135000-56141800	Strong transcription	Fetal Intestine Small	intestine
28	chr7:56135000-56142600	Strong transcription	Fetal Stomach	stomach
29	chr7:56135400-56141000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr7:56135800-56141000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:56135800-56141800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:56136000-56141000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:56136000-56141000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:56136000-56141000	Strong transcription	Liver	Liver
35	chr7:56136000-56141000	Strong transcription	Thymus	Thymus
36	chr7:56136000-56141200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:56136000-56141200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr7:56136000-56141400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:56136000-56142200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:56136200-56141000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:56136200-56141000	Strong transcription	Ovary	ovary
42	chr7:56136200-56141200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:56136200-56141600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:56136200-56142000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:56136200-56142000	Strong transcription	Fetal Brain Female	brain
46	chr7:56137000-56141600	Weak transcription	K562	blood
47	chr7:56137200-56146000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr7:56137600-56141800	Weak transcription	Pancreas	Pancrea
49	chr7:56138200-56144200	Weak transcription	Hela-S3	cervix
50	chr7:56138600-56142000	Weak transcription	Muscle Satellite Cultured Cells	--

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