Variant report

Variant	rs1037529
Chromosome Location	chr8:98942017-98942018
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	FOXA2	chr8:98941965-98942172	HepG2	liver:	n/a	n/a
2	SMC3	chr8:98942003-98942260	Hela-S3	cervix:	n/a	chr8:98942126-98942133
3	MAZ	chr8:98941977-98942177	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr8:98941970-98942209	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr8:98941981-98942181	SK-N-SH_RA	brain:	n/a	n/a
6	FOXA1	chr8:98941915-98942196	T-47D	breast:	n/a	n/a
7	FOXA1	chr8:98941846-98942244	HepG2	liver:	n/a	n/a
8	RCOR1	chr8:98940834-98942069	IMR90	lung:	n/a	n/a
9	FOXA1	chr8:98941911-98942166	T-47D	breast:	n/a	n/a
10	RAD21	chr8:98941872-98942383	MCF-7	breast:	n/a	n/a
11	CTCF	chr8:98941960-98942292	GM12878	blood:	n/a	n/a
12	RAD21	chr8:98941844-98942331	MCF-7	breast:	n/a	n/a
13	FOXA1	chr8:98941855-98942178	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:98940343..98943382-chr8:99056246..99058981,3	MCF-7	breast:
2	chr8:98936307..98939164-chr8:98941664..98943484,3	K562	blood:

Variant related genes	Relation type
MATN2	TF binding region
ENSG00000156482	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10755895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290470	0.89[CEU][hapmap]
rs2331806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2331808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35909550	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4735511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4735512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4735513	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1037529	MTDH	cis	parietal	SCAN
rs1037529	MATN2	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98929200-98944800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:98930800-98950000	Weak transcription	Right Ventricle	heart
3	chr8:98931200-98944200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:98931800-98943200	Enhancers	Fetal Muscle Leg	muscle
5	chr8:98932200-98943400	Weak transcription	Pancreas	Pancrea
6	chr8:98934200-98943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:98935200-98944400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:98938200-98944400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr8:98938200-98956200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr8:98938200-98969200	Weak transcription	Colonic Mucosa	Colon
11	chr8:98938400-98943200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr8:98938400-98943600	Weak transcription	Fetal Kidney	kidney
13	chr8:98938600-98943000	Weak transcription	Fetal Heart	heart
14	chr8:98938600-98943400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr8:98938600-98944400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:98938800-98943400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:98938800-98944400	Weak transcription	Left Ventricle	heart
18	chr8:98939000-98943200	Weak transcription	Placenta	Placenta
19	chr8:98939000-98943400	Weak transcription	Fetal Intestine Small	intestine
20	chr8:98939000-98944400	Weak transcription	Right Atrium	heart
21	chr8:98939000-98944400	Weak transcription	Stomach Mucosa	stomach
22	chr8:98939200-98942200	Weak transcription	Liver	Liver
23	chr8:98939200-98943600	Weak transcription	Fetal Intestine Large	intestine
24	chr8:98940000-98942600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:98940000-98943600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:98940200-98947400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr8:98940800-98942200	Enhancers	Colon Smooth Muscle	Colon
28	chr8:98940800-98942200	Enhancers	Fetal Stomach	stomach
29	chr8:98940800-98942400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr8:98940800-98942400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:98940800-98942400	Enhancers	NHLF	lung
32	chr8:98940800-98942600	Enhancers	Brain Hippocampus Middle	brain
33	chr8:98940800-98942600	Enhancers	Brain Substantia Nigra	brain
34	chr8:98940800-98943200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr8:98940800-98944600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:98941000-98942200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr8:98941000-98942200	Enhancers	Brain Cingulate Gyrus	brain
38	chr8:98941000-98942400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr8:98941000-98968000	Weak transcription	Esophagus	oesophagus
40	chr8:98941200-98942200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr8:98941200-98942200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr8:98941200-98942200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr8:98941200-98942200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:98941200-98942200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:98941200-98942200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr8:98941200-98942200	Enhancers	HSMM	muscle
47	chr8:98941200-98942400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr8:98941200-98942400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:98941200-98942400	Enhancers	Adipose Nuclei	Adipose
50	chr8:98941200-98942400	Enhancers	Brain Anterior Caudate	brain

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