Variant report

Variant	rs342114
Chromosome Location	chr2:20664705-20664706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20664615..20666200-chr2:20700420..20703314,2	MCF-7	breast:
2	chr2:20664203..20670367-chr2:20692234..20698325,8	MCF-7	breast:
3	chr2:20664607..20668124-chr2:20695979..20697916,4	MCF-7	breast:
4	chr2:20642734..20659399-chr2:20663729..20679011,83	MCF-7	breast:
5	chr2:20643286..20659825-chr2:20662702..20680153,143	MCF-7	breast:
6	chr2:20664677..20667421-chr2:20834049..20837198,4	MCF-7	breast:
7	chr2:20664006..20666925-chr2:20834002..20835809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227047	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1002162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10204085	0.92[JPT][hapmap]
rs10205221	0.80[CEU][hapmap]
rs1062292	0.87[CHD][hapmap]
rs11898154	0.92[CEU][hapmap]
rs11901246	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs12988451	0.80[CEU][hapmap]
rs13021908	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs1453051	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168195	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872070	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs2084919	0.85[CEU][hapmap]
rs342057	0.81[CEU][hapmap]
rs342105	0.93[ASW][hapmap];0.82[CEU][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap]
rs342106	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342109	0.90[AFR][1000 genomes]
rs342110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs342111	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs342113	0.83[AFR][1000 genomes]
rs342116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342117	0.82[CEU][hapmap]
rs342118	0.87[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs342119	0.81[CEU][hapmap]
rs342123	0.84[CEU][hapmap]
rs342124	0.85[CEU][hapmap]
rs342125	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs342126	0.84[CEU][hapmap]
rs4666308	0.81[CEU][hapmap]
rs4666396	0.93[CHD][hapmap]
rs4666398	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666401	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4666402	0.80[CEU][hapmap]
rs6531240	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704834	0.82[GIH][hapmap]
rs674534	0.85[CEU][hapmap]
rs715670	0.80[CEU][hapmap]
rs7601359	0.85[ASN][1000 genomes]
rs959058	0.81[CEU][hapmap]
rs9917322	0.80[CEU][hapmap]

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	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs342114	FAM49A	cis	cerebellum	SCAN
rs342114	HS1BP3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20653200-20666200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:20653400-20666400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:20653400-20674000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:20654000-20665400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:20656200-20671800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:20657200-20665800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:20658400-20665400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:20659000-20665400	Weak transcription	Esophagus	oesophagus
9	chr2:20659200-20665400	Weak transcription	Gastric	stomach
10	chr2:20659200-20665400	Weak transcription	Pancreas	Pancrea
11	chr2:20659200-20665400	Weak transcription	Stomach Mucosa	stomach
12	chr2:20660800-20667200	Weak transcription	Lung	lung
13	chr2:20664400-20672400	Weak transcription	Right Atrium	heart

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