Variant report

Variant	rs2675117
Chromosome Location	chr2:183936915-183936916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:183936424..183941841-chr2:183941943..183946520,8	K562	blood:

Variant related genes	Relation type
ENSG00000162999	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10170163	0.81[ASN][1000 genomes]
rs10183561	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10460315	0.83[ASN][1000 genomes]
rs11692613	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12463411	0.83[ASN][1000 genomes]
rs12693331	0.90[ASN][1000 genomes]
rs13399265	0.83[ASN][1000 genomes]
rs16823717	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs16823721	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs16823967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823970	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs16823971	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs16823974	1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs16823976	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16824001	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1812647	0.83[ASN][1000 genomes]
rs2138482	0.83[ASN][1000 genomes]
rs2138484	1.00[CHB][hapmap]
rs2138485	0.88[ASN][1000 genomes]
rs2247840	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2368335	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2368354	0.86[ASN][1000 genomes]
rs2705714	0.85[ASN][1000 genomes]
rs2944346	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[ASN][1000 genomes]
rs2952345	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3748879	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs4597478	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4666607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666885	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs55942934	0.96[ASN][1000 genomes]
rs56271556	0.96[ASN][1000 genomes]
rs59041013	0.96[ASN][1000 genomes]
rs61283216	0.96[ASN][1000 genomes]
rs61526412	0.96[ASN][1000 genomes]
rs6742203	0.90[ASN][1000 genomes]
rs73035651	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73036601	0.96[ASN][1000 genomes]
rs867340	0.84[ASN][1000 genomes]
rs925805	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv961916	chr2:183936537-183937037	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2675117	FRZB	cis	cerebellum	SCAN
rs2675117	NCBP1	trans	parietal	SCAN
rs2675117	ZC3H15	cis	parietal	SCAN
rs2675117	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2675117	NCKAP1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183934800-183943000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:183934800-183943000	Weak transcription	Esophagus	oesophagus
3	chr2:183934800-183943000	Weak transcription	Right Atrium	heart
4	chr2:183935600-183937200	Enhancers	Pancreas	Pancrea
5	chr2:183935800-183943000	Weak transcription	Aorta	Aorta
6	chr2:183936400-183940200	Weak transcription	Gastric	stomach
7	chr2:183936400-183943000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:183936400-183943000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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