Variant report

Variant	rs56209613
Chromosome Location	chr4:8268405-8268406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr4:8267759-8268712	IMR90	lung:	n/a	n/a
2	JUND	chr4:8268048-8268633	K562	blood:	n/a	chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268378-8268390 chr4:8268380-8268388 chr4:8268379-8268389 chr4:8268376-8268387
3	JUN	chr4:8267752-8268675	K562	blood:	n/a	chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268458-8268471 chr4:8268378-8268390 chr4:8268380-8268388 chr4:8268379-8268389 chr4:8268376-8268387
4	JUN	chr4:8268236-8268648	K562	blood:	n/a	chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268458-8268471 chr4:8268378-8268390 chr4:8268380-8268388 chr4:8268379-8268389 chr4:8268376-8268387
5	CTCF	chr4:8268340-8268490	HUVEC	blood vessel:	n/a	n/a
6	JUND	chr4:8268250-8268634	HepG2	liver:	n/a	chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268378-8268390 chr4:8268380-8268388 chr4:8268379-8268389 chr4:8268376-8268387
7	EGR1	chr4:8268222-8268536	K562	blood:	n/a	chr4:8268337-8268352
8	CTCF	chr4:8268380-8268530	GM12866	blood:	n/a	n/a
9	JUN	chr4:8268339-8268643	HepG2	liver:	n/a	chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268379-8268389 chr4:8268458-8268471 chr4:8268378-8268390 chr4:8268380-8268388 chr4:8268379-8268389 chr4:8268376-8268387

No.	Distal block	Cell Line	Cell type
1	chr4:8268241..8269567-chr4:8404622..8405485,4	MCF-7	breast:
2	chr4:8261994..8265646-chr4:8266271..8270310,6	MCF-7	breast:
3	chr4:8244003..8244602-chr4:8267775..8268462,2	MCF-7	breast:
4	chr4:8261913..8264810-chr4:8267913..8270603,2	K562	blood:
5	chr4:8266213..8269192-chr4:8274192..8276756,2	K562	blood:

Variant related genes	Relation type
HTRA3	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10805205	0.81[ASN][1000 genomes]
rs11727999	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11933867	0.81[ASN][1000 genomes]
rs12507774	0.90[ASN][1000 genomes]
rs4643793	0.96[ASN][1000 genomes]
rs55954316	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56398646	0.91[ASN][1000 genomes]
rs58713023	0.84[ASN][1000 genomes]
rs62286483	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases
4	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv593627	chr4:8202211-8311043	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv878600	chr4:8209447-8312158	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	esv1794365	chr4:8254784-8271983	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
16	esv1797624	chr4:8254784-8271983	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	esv1801002	chr4:8254784-8271983	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	nsv461218	chr4:8254784-8320126	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv593628	chr4:8254784-8320126	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56209613	SH3TC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8249800-8268600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:8254800-8271600	Weak transcription	Gastric	stomach
3	chr4:8258000-8271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:8263000-8268600	Weak transcription	A549	lung
5	chr4:8263000-8269200	Weak transcription	Esophagus	oesophagus
6	chr4:8263800-8270800	Weak transcription	Lung	lung
7	chr4:8264200-8268600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:8264200-8268800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:8264800-8268600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:8264800-8268800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:8265400-8269200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:8266800-8269800	Enhancers	Stomach Mucosa	stomach
13	chr4:8267000-8268800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:8267200-8269600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:8267800-8269800	Enhancers	Fetal Muscle Leg	muscle
16	chr4:8268000-8271200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:8268200-8269600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:8268200-8269600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:8268200-8269600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:8268200-8270200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr4:8268200-8272200	Enhancers	Fetal Heart	heart
22	chr4:8268400-8268600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:8268400-8268600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr4:8268400-8269000	Enhancers	K562	blood
25	chr4:8268400-8269200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr4:8268400-8269200	Enhancers	Fetal Lung	lung
27	chr4:8268400-8269400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:8268400-8269400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:8268400-8269400	Enhancers	Left Ventricle	heart
30	chr4:8268400-8269400	Enhancers	Ovary	ovary
31	chr4:8268400-8269400	Enhancers	Right Atrium	heart
32	chr4:8268400-8269600	Enhancers	Adipose Nuclei	Adipose
33	chr4:8268400-8269600	Enhancers	Placenta	Placenta
34	chr4:8268400-8269600	Enhancers	Fetal Stomach	stomach
35	chr4:8268400-8269600	Enhancers	Pancreas	Pancrea
36	chr4:8268400-8269600	Enhancers	Right Ventricle	heart
37	chr4:8268400-8270800	Enhancers	Stomach Smooth Muscle	stomach
38	chr4:8268400-8271000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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