Variant report

Variant	rs56398646
Chromosome Location	chr4:8264582-8264583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8252135..8254748-chr4:8262223..8264616,3	K562	blood:
2	chr4:8261994..8265646-chr4:8266271..8270310,6	MCF-7	breast:
3	chr4:8261913..8264810-chr4:8267913..8270603,2	K562	blood:
4	chr4:8261537..8264221-chr4:8264274..8265849,2	MCF-7	breast:
5	chr4:8252135..8255007-chr4:8262927..8264616,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10755198	0.82[EUR][1000 genomes]
rs10805204	0.82[EUR][1000 genomes]
rs10805205	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11727999	0.87[ASN][1000 genomes]
rs11933867	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12507774	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678336	0.83[EUR][1000 genomes]
rs4643793	0.87[ASN][1000 genomes]
rs55811424	0.81[EUR][1000 genomes]
rs56116912	0.81[ASN][1000 genomes]
rs56209613	0.91[ASN][1000 genomes]
rs57240686	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58713023	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62286481	0.84[AMR][1000 genomes]
rs62286483	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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
20	esv3376319	chr4:8263077-8265925	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56398646	SH3TC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8249800-8268400	Weak transcription	Right Atrium	heart
2	chr4:8249800-8268600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:8254800-8271600	Weak transcription	Gastric	stomach
4	chr4:8256000-8264800	Enhancers	Fetal Muscle Leg	muscle
5	chr4:8258000-8271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:8259600-8264800	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:8259600-8264800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:8260400-8265400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:8261400-8265400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:8261800-8264600	Enhancers	Placenta	Placenta
11	chr4:8261800-8265400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:8262600-8264600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:8262600-8265200	Enhancers	Spleen	Spleen
14	chr4:8262800-8264800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:8262800-8265400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:8263000-8264800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr4:8263000-8268200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:8263000-8268400	Weak transcription	Fetal Lung	lung
19	chr4:8263000-8268400	Weak transcription	Right Ventricle	heart
20	chr4:8263000-8268600	Weak transcription	A549	lung
21	chr4:8263000-8269200	Weak transcription	Esophagus	oesophagus
22	chr4:8263200-8265000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:8263200-8268400	Weak transcription	Adipose Nuclei	Adipose
24	chr4:8263200-8268400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:8263600-8264600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:8263800-8268000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:8263800-8270800	Weak transcription	Lung	lung
28	chr4:8264000-8265400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:8264000-8266000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:8264200-8264600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:8264200-8268600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:8264200-8268800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:8264400-8265000	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr4:8264400-8265400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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