Variant report

Variant	rs2529179
Chromosome Location	chr7:101350790-101350791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101350597..101352580-chr7:101511716..101513955,2	K562	blood:
2	chr7:101346602..101348960-chr7:101350465..101352401,2	MCF-7	breast:
3	chr7:101344436..101347145-chr7:101349476..101351010,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12534998	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12535663	0.88[ASN][1000 genomes]
rs1722207	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1965519	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs1969432	0.92[ASN][1000 genomes]
rs2429068	0.89[ASN][1000 genomes]
rs2529181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2529182	1.00[ASN][1000 genomes]
rs2529185	0.85[CHB][hapmap]
rs2529186	0.89[ASN][1000 genomes]
rs2529187	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2529188	0.89[ASN][1000 genomes]
rs2529189	0.89[ASN][1000 genomes]
rs2529190	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2529238	0.85[JPT][hapmap]
rs2529240	0.82[ASN][1000 genomes]
rs2529241	0.82[ASN][1000 genomes]
rs2529242	0.92[ASN][1000 genomes]
rs2529243	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2529246	1.00[ASN][1000 genomes]
rs2529247	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690887	0.90[CHB][hapmap]
rs2690890	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2690891	0.99[ASN][1000 genomes]
rs2690892	0.99[ASN][1000 genomes]
rs2690893	0.99[ASN][1000 genomes]
rs2690896	0.95[ASN][1000 genomes]
rs2690902	0.91[ASN][1000 genomes]
rs940479	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv831079	chr7:101273495-101466776	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1021797	chr7:101342353-101466957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv539046	chr7:101342353-101466957	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2529179	FAM200A	cis	cerebellum	SCAN
rs2529179	BAIAP2L1	cis	parietal	SCAN
rs2529179	LRCH4	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101332000-101376800	Weak transcription	Right Atrium	heart
2	chr7:101349600-101352000	Enhancers	Stomach Mucosa	stomach
3	chr7:101350000-101350800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:101350000-101350800	Enhancers	Gastric	stomach
5	chr7:101350000-101350800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr7:101350000-101351600	Enhancers	Colonic Mucosa	Colon
7	chr7:101350000-101352600	Enhancers	Fetal Intestine Large	intestine
8	chr7:101350200-101350800	Enhancers	Duodenum Mucosa	Duodenum
9	chr7:101350200-101352000	Enhancers	Fetal Intestine Small	intestine
10	chr7:101350400-101351000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr7:101350400-101351000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr7:101350400-101351000	Bivalent Enhancer	HepG2	liver
13	chr7:101350600-101350800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr7:101350600-101351800	Enhancers	Esophagus	oesophagus

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