Variant report

Variant	rs256946
Chromosome Location	chr5:114931610-114931611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114930059..114933098-chr5:114935094..114939412,3	K562	blood:
2	chr5:114930114..114932547-chr5:114952290..114954569,2	K562	blood:
3	chr5:114925661..114928163-chr5:114931271..114933009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243414	Chromatin interaction
ENSG00000249249	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10077825	0.85[CEU][hapmap]
rs11740401	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11743277	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1363550	0.87[AMR][1000 genomes]
rs1422641	0.87[AMR][1000 genomes]
rs1422642	0.81[AMR][1000 genomes]
rs1422643	0.87[AMR][1000 genomes]
rs1422644	0.87[AMR][1000 genomes]
rs1592942	0.87[AMR][1000 genomes]
rs1592943	0.87[AMR][1000 genomes]
rs17137937	0.85[ASN][1000 genomes]
rs17138030	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs185379	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895283	0.87[AMR][1000 genomes]
rs194398	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1978441	0.89[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2052504	0.87[AMR][1000 genomes]
rs2052505	0.87[AMR][1000 genomes]
rs2288384	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2431600	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2546473	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2546483	0.82[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes]
rs256958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs256960	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256961	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256966	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256973	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256974	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256975	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256979	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256981	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256982	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256983	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256985	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256992	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2597	1.00[ASN][1000 genomes]
rs2617441	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34986301	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4920867	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4920869	0.93[ASN][1000 genomes]
rs4920873	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57010629	0.91[ASN][1000 genomes]
rs57028257	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58301336	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60640600	0.84[ASN][1000 genomes]
rs72817155	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73254600	0.91[ASN][1000 genomes]
rs73264735	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73782714	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7702747	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9326965	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9968571	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs256946	TICAM2	cis	parietal	SCAN
rs256946	KLK10	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114911200-114935600	Weak transcription	Gastric	stomach
2	chr5:114913000-114935200	Weak transcription	Aorta	Aorta
3	chr5:114914400-114936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:114914800-114937400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:114919800-114935600	Weak transcription	NH-A	brain
6	chr5:114921600-114935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:114921600-114935400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:114925000-114934000	Weak transcription	GM12878-XiMat	blood
9	chr5:114925000-114935200	Weak transcription	Left Ventricle	heart
10	chr5:114925000-114937400	Weak transcription	Pancreas	Pancrea
11	chr5:114926800-114932400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:114930200-114935000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:114930200-114937400	Weak transcription	Hela-S3	cervix
14	chr5:114930400-114934800	Weak transcription	Adipose Nuclei	Adipose
15	chr5:114930600-114932800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:114930600-114936400	Weak transcription	HUVEC	blood vessel
17	chr5:114930800-114933400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:114930800-114935200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:114930800-114935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:114930800-114935400	Weak transcription	HSMM	muscle
21	chr5:114930800-114935600	Weak transcription	Fetal Brain Female	brain
22	chr5:114931000-114932600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:114931000-114934600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:114931000-114935000	Weak transcription	NHLF	lung
25	chr5:114931000-114935200	Weak transcription	Psoas Muscle	Psoas
26	chr5:114931000-114936800	Weak transcription	Fetal Brain Male	brain
27	chr5:114931200-114933400	Weak transcription	NHDF-Ad	bronchial
28	chr5:114931200-114935200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:114931600-114931800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:114931600-114932600	Weak transcription	Osteobl	bone
31	chr5:114931600-114935200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:114931600-114937000	Weak transcription	Fetal Intestine Small	intestine

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