Variant report

Variant	rs12431896
Chromosome Location	chr14:78088813-78088814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78085465..78087212-chr14:78088002..78090787,2	MCF-7	breast:
2	chr14:78081471..78084172-chr14:78085456..78089747,4	K562	blood:
3	chr14:78085500..78087936-chr14:78087989..78089508,2	K562	blood:
4	chr14:77935677..77938460-chr14:78087456..78089168,2	MCF-7	breast:
5	chr14:78081712..78085170-chr14:78085494..78089373,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100596	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12431525	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12433198	1.00[ASW][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12433954	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12434701	0.93[ASN][1000 genomes]
rs12436803	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs176895	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751876	1.00[ASW][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17751917	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17751923	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17751980	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17751993	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752262	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17752707	1.00[MKK][hapmap]
rs17824984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17825014	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17825229	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs17825235	1.00[CHB][hapmap]
rs2142187	0.85[JPT][hapmap]
rs2178877	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2364578	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2886122	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs2886132	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35389286	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4497612	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55697089	1.00[AFR][1000 genomes]
rs55776552	1.00[AFR][1000 genomes]
rs55799811	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56264628	1.00[AFR][1000 genomes]
rs56286233	1.00[AFR][1000 genomes]
rs58312042	0.90[ASN][1000 genomes]
rs59721556	0.90[ASN][1000 genomes]
rs7159486	0.95[EUR][1000 genomes];0.80[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12431896	ADCK1	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78083000-78089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:78083200-78089400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:78083800-78091600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:78086600-78089000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr14:78088200-78090000	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr14:78088600-78089800	Enhancers	Fetal Intestine Large	intestine
7	chr14:78088600-78089800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr14:78088600-78090000	Enhancers	Duodenum Mucosa	Duodenum
9	chr14:78088800-78089800	Enhancers	Fetal Intestine Small	intestine
10	chr14:78088800-78089800	Enhancers	Placenta	Placenta
11	chr14:78088800-78090000	Enhancers	Stomach Mucosa	stomach

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