Variant report

Variant	rs11727999
Chromosome Location	chr4:8268700-8268701
allele	A/G
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	CTCF	chr4:8268669-8269529	HCT-116	colon:	n/a	chr4:8269082-8269092 chr4:8269077-8269095 chr4:8269078-8269094 chr4:8269080-8269093
3	SMC3	chr4:8268574-8269494	SK-N-SH	brain:	n/a	chr4:8269079-8269093 chr4:8269083-8269093
4	CTCF	chr4:8268616-8269437	A549	lung:	n/a	chr4:8269082-8269092 chr4:8269077-8269095 chr4:8269078-8269094 chr4:8269080-8269093
5	CTCF	chr4:8268640-8268790	GM12868	blood:	n/a	n/a
6	RAD21	chr4:8268563-8269459	SK-N-SH	brain:	n/a	chr4:8269081-8269094 chr4:8269083-8269093
7	RAD21	chr4:8268657-8269530	HCT-116	colon:	n/a	chr4:8269081-8269094 chr4:8269083-8269093
8	HMGN3	chr4:8268641-8269275	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8268685..8271204-chr4:8420095..8422355,2	MCF-7	breast:
2	chr4:8268241..8269567-chr4:8404622..8405485,4	MCF-7	breast:
3	chr4:8261994..8265646-chr4:8266271..8270310,6	MCF-7	breast:
4	chr4:8261913..8264810-chr4:8267913..8270603,2	K562	blood:
5	chr4:8266213..8269192-chr4:8274192..8276756,2	K562	blood:
6	chr4:8268637..8269538-chr4:8412094..8412713,3	MCF-7	breast:
7	chr4:8268620..8269557-chr4:8404343..8405485,5	K562	blood:
8	chr4:8268593..8269552-chr4:8403907..8405561,11	MCF-7	breast:

Variant related genes	Relation type
HTRA3	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12507774	0.86[ASN][1000 genomes]
rs4643793	0.91[ASN][1000 genomes]
rs55858728	0.82[ASN][1000 genomes]
rs55954316	0.82[EUR][1000 genomes]
rs56209613	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56398646	0.87[ASN][1000 genomes]
rs62286483	0.85[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
rs11727999	SH3TC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8254800-8271600	Weak transcription	Gastric	stomach
2	chr4:8258000-8271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:8263000-8269200	Weak transcription	Esophagus	oesophagus
4	chr4:8263800-8270800	Weak transcription	Lung	lung
5	chr4:8264200-8268800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:8264800-8268800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:8265400-8269200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:8266800-8269800	Enhancers	Stomach Mucosa	stomach
9	chr4:8267000-8268800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:8267200-8269600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr4:8267800-8269800	Enhancers	Fetal Muscle Leg	muscle
12	chr4:8268000-8271200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:8268200-8269600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:8268200-8269600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:8268200-8269600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:8268200-8270200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr4:8268200-8272200	Enhancers	Fetal Heart	heart
18	chr4:8268400-8269000	Enhancers	K562	blood
19	chr4:8268400-8269200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr4:8268400-8269200	Enhancers	Fetal Lung	lung
21	chr4:8268400-8269400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:8268400-8269400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:8268400-8269400	Enhancers	Left Ventricle	heart
24	chr4:8268400-8269400	Enhancers	Ovary	ovary
25	chr4:8268400-8269400	Enhancers	Right Atrium	heart
26	chr4:8268400-8269600	Enhancers	Adipose Nuclei	Adipose
27	chr4:8268400-8269600	Enhancers	Placenta	Placenta
28	chr4:8268400-8269600	Enhancers	Fetal Stomach	stomach
29	chr4:8268400-8269600	Enhancers	Pancreas	Pancrea
30	chr4:8268400-8269600	Enhancers	Right Ventricle	heart
31	chr4:8268400-8270800	Enhancers	Stomach Smooth Muscle	stomach
32	chr4:8268400-8271000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:8268600-8269000	Enhancers	Fetal Intestine Small	intestine
34	chr4:8268600-8269200	Enhancers	HUVEC	blood vessel
35	chr4:8268600-8269400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr4:8268600-8269400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:8268600-8269400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:8268600-8269600	Enhancers	Colon Smooth Muscle	Colon
39	chr4:8268600-8269600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr4:8268600-8269600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:8268600-8269600	Enhancers	A549	lung

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