Variant report

Variant	rs11677205
Chromosome Location	chr2:48537416-48537417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr2:48537403-48538154	K562	blood:	n/a	n/a
2	POLR2A	chr2:48537402-48537566	MCF10A-Er-Src	breast:	n/a	n/a
3	KAP1	chr2:48537371-48538940	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48496037..48498281-chr2:48536801..48539296,2	K562	blood:
2	chr2:48518431..48520376-chr2:48536529..48538446,2	K562	blood:
3	chr2:48536399..48538424-chr2:48545720..48548096,2	K562	blood:
4	chr2:48536558..48539555-chr2:48539697..48542040,2	K562	blood:
5	chr2:48535868..48537728-chr2:48543055..48544951,2	K562	blood:

No data

Variant related genes	Relation type
FOXN2	TF binding region
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10195717	1.00[CEU][hapmap]
rs11674217	0.88[CEU][hapmap]
rs11674317	0.80[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11676925	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11678934	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs11679518	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11680657	0.84[EUR][1000 genomes]
rs11680968	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11682838	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11683202	0.85[TSI][hapmap]
rs11687276	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11687401	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11687461	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11687851	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11689285	0.88[CEU][hapmap]
rs11691302	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11691407	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11692537	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs11694094	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11695923	0.84[EUR][1000 genomes]
rs13398456	1.00[CEU][hapmap]
rs17325209	0.85[EUR][1000 genomes]
rs17396793	0.80[CEU][hapmap]
rs17397094	0.84[EUR][1000 genomes]
rs17397449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2014675	0.84[EUR][1000 genomes]
rs28505584	0.82[EUR][1000 genomes]
rs2937	0.88[CEU][hapmap]
rs4530419	0.80[CEU][hapmap]
rs6733558	0.80[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs6747738	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7573281	0.82[EUR][1000 genomes]
rs7583719	0.80[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs7584796	0.82[EUR][1000 genomes]
rs952468	1.00[CEU][hapmap];0.84[EUR][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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11677205	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48506000-48539000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:48528000-48539200	Weak transcription	Primary T cells from cord blood	blood
3	chr2:48530200-48540200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:48533000-48539800	Weak transcription	Primary B cells from cord blood	blood
5	chr2:48534400-48538800	Weak transcription	NHEK	skin
6	chr2:48534400-48540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:48534600-48539200	Weak transcription	Hela-S3	cervix
8	chr2:48534600-48540200	Weak transcription	Adipose Nuclei	Adipose
9	chr2:48534600-48540200	Weak transcription	NHDF-Ad	bronchial
10	chr2:48534800-48539600	Weak transcription	Placenta	Placenta
11	chr2:48534800-48539600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:48534800-48539600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:48535000-48538400	Weak transcription	HepG2	liver
14	chr2:48535600-48540400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:48535800-48539400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:48535800-48539600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:48535800-48539600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:48536400-48539400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:48537400-48539200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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