Variant report

Variant	rs7140030
Chromosome Location	chr13:111064159-111064160
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	RAD21	chr13:111063923-111065207	IMR90	lung:	n/a	n/a
2	ZNF263	chr13:111064159-111064854	HEK293-T-REx	kidney:	n/a	n/a
3	RAD21	chr13:111063415-111065761	SK-N-SH	brain:	n/a	chr13:111063778-111063791 chr13:111063771-111063785 chr13:111063770-111063784
4	SMC3	chr13:111063802-111065550	SK-N-SH	brain:	n/a	chr13:111064765-111064779
5	FOS	chr13:111064147-111064948	HUVEC	blood vessel:	n/a	chr13:111064671-111064678 chr13:111064670-111064678 chr13:111064668-111064679 chr13:111064669-111064678 chr13:111064670-111064679 chr13:111064668-111064680
6	MXI1	chr13:111064148-111064204	GM12878	blood:	n/a	n/a
7	CHD1	chr13:111063393-111066220	IMR90	lung:	n/a	n/a
8	POLR2A	chr13:111063567-111065229	IMR90	lung:	n/a	n/a
9	KAP1	chr13:111063793-111065238	U2OS	brain:	n/a	chr13:111063939-111063947 chr13:111064668-111064677 chr13:111064671-111064680

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111063956..111066256-chr13:111066546..111068934,2	K562	blood:

Variant related genes	Relation type
ENSG00000238629	TF binding region
ENSG00000238629	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12853693	0.80[EUR][1000 genomes]
rs34402154	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34992019	0.80[EUR][1000 genomes]
rs35096048	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56687994	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492267	0.85[EUR][1000 genomes]
rs7140025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7318742	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320498	0.82[EUR][1000 genomes]
rs7323228	0.88[ASW][hapmap]
rs7328731	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7983374	0.83[TSI][hapmap]
rs7991842	0.80[MEX][hapmap]
rs913397	0.90[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7140030	STAM	trans	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111050200-111064400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:111050200-111066000	Enhancers	NHDF-Ad	bronchial
3	chr13:111050200-111075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:111056200-111066000	Enhancers	Lung	lung
5	chr13:111057800-111064800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr13:111057800-111070400	Enhancers	Right Atrium	heart
7	chr13:111058000-111066000	Enhancers	HUVEC	blood vessel
8	chr13:111058800-111064200	Weak transcription	Fetal Intestine Large	intestine
9	chr13:111059400-111065200	Enhancers	Spleen	Spleen
10	chr13:111059400-111067000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:111059600-111064200	Genic enhancers	Osteobl	bone
12	chr13:111059600-111064400	Enhancers	Aorta	Aorta
13	chr13:111059800-111064800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:111059800-111065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:111060200-111064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:111060200-111064200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr13:111060200-111064400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:111060200-111064400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr13:111060200-111065200	Enhancers	HMEC	breast
20	chr13:111060200-111065600	Weak transcription	Esophagus	oesophagus
21	chr13:111060200-111067000	Enhancers	Right Ventricle	heart
22	chr13:111060200-111082800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:111060400-111064200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr13:111060400-111064400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:111060400-111064800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:111061000-111065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:111061000-111077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:111061200-111064200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:111061200-111065800	Enhancers	Colon Smooth Muscle	Colon
30	chr13:111061400-111064800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:111061400-111065600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:111061400-111065600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:111061400-111065800	Enhancers	Rectal Smooth Muscle	rectum
34	chr13:111061600-111064200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:111061600-111064200	Weak transcription	Pancreas	Pancrea
36	chr13:111061600-111065200	Enhancers	Fetal Kidney	kidney
37	chr13:111061600-111065800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:111061600-111069200	Weak transcription	Fetal Brain Male	brain
39	chr13:111061800-111064400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr13:111061800-111064800	Enhancers	NH-A	brain
41	chr13:111061800-111066000	Enhancers	HSMM	muscle
42	chr13:111061800-111066200	Enhancers	NHLF	lung
43	chr13:111061800-111066800	Enhancers	Placenta	Placenta
44	chr13:111062000-111065800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr13:111062000-111065800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr13:111062000-111069000	Enhancers	Left Ventricle	heart
47	chr13:111062200-111064200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr13:111062400-111064200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:111062400-111066000	Enhancers	Ovary	ovary
50	chr13:111062600-111064200	Enhancers	Muscle Satellite Cultured Cells	--

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