Variant report

Variant	rs1281096
Chromosome Location	chr4:8249403-8249404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8247640..8250580-chr4:8396679..8398196,2	K562	blood:
2	chr4:8247491..8249787-chr4:8251476..8253386,2	MCF-7	breast:
3	chr4:8243003..8245939-chr4:8248896..8251754,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10938701	0.82[EUR][1000 genomes]
rs12186177	0.85[EUR][1000 genomes]
rs12186205	0.81[EUR][1000 genomes]
rs12650149	0.82[EUR][1000 genomes]
rs1281097	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281098	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281100	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678335	0.87[EUR][1000 genomes]
rs1712292	0.89[EUR][1000 genomes]
rs1712296	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2291071	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3852111	0.89[EUR][1000 genomes]
rs4696783	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696784	0.85[EUR][1000 genomes]
rs4696785	0.87[EUR][1000 genomes]
rs4696786	0.84[EUR][1000 genomes]
rs62286480	0.85[EUR][1000 genomes]
rs62286482	0.85[EUR][1000 genomes]
rs6828322	0.86[EUR][1000 genomes]
rs7654812	0.80[EUR][1000 genomes]
rs7655174	0.84[EUR][1000 genomes]
rs7676690	0.85[EUR][1000 genomes]
rs7679075	0.80[EUR][1000 genomes]
rs7692203	0.85[EUR][1000 genomes]
rs7694755	0.85[EUR][1000 genomes]
rs922517	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	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	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv878598	chr4:8195705-8254784	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	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
12	esv2763338	chr4:8199091-8260812	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1281096	SH3TC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8240800-8254400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:8241400-8254200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:8245000-8249800	Weak transcription	HUVEC	blood vessel
4	chr4:8245000-8255800	Weak transcription	HMEC	breast
5	chr4:8245200-8255200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:8246200-8254400	Weak transcription	Fetal Thymus	thymus
7	chr4:8247600-8250000	Enhancers	Lung	lung
8	chr4:8247800-8250000	Enhancers	Liver	Liver
9	chr4:8248000-8249800	Enhancers	Right Atrium	heart
10	chr4:8248000-8250000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:8248000-8250000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr4:8248000-8250000	Enhancers	Fetal Muscle Leg	muscle
13	chr4:8248200-8250000	Enhancers	Placenta	Placenta
14	chr4:8248200-8250000	Enhancers	Left Ventricle	heart
15	chr4:8248400-8250600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:8248600-8249600	Enhancers	NHDF-Ad	bronchial
17	chr4:8248600-8249800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:8248600-8249800	Enhancers	Right Ventricle	heart
19	chr4:8248600-8249800	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr4:8248600-8250000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:8248600-8250000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:8248600-8250000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr4:8248600-8250000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:8248600-8250200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:8248600-8250200	Enhancers	Fetal Lung	lung
26	chr4:8248800-8250000	Bivalent Enhancer	NHLF	lung
27	chr4:8248800-8251800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:8249000-8249600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:8249000-8249600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr4:8249000-8249800	Enhancers	HSMM	muscle
31	chr4:8249000-8250000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:8249000-8250000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr4:8249000-8254400	Weak transcription	Gastric	stomach
34	chr4:8249200-8249600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:8249200-8249600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:8249200-8249800	Enhancers	Fetal Intestine Small	intestine
37	chr4:8249200-8249800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr4:8249200-8250000	Enhancers	HSMMtube	muscle
39	chr4:8249400-8249600	Enhancers	Stomach Mucosa	stomach
40	chr4:8249400-8249600	Flanking Active TSS	Hela-S3	cervix
41	chr4:8249400-8249800	Enhancers	Esophagus	oesophagus
42	chr4:8249400-8249800	Enhancers	Fetal Muscle Trunk	muscle
43	chr4:8249400-8249800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
44	chr4:8249400-8249800	Flanking Active TSS	A549	lung
45	chr4:8249400-8250000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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