Variant report

Variant	rs13147611
Chromosome Location	chr4:147231187-147231188
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	chr4:147228585..147230437-chr4:147230480..147232444,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10011474	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10012369	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10212750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107111	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121171	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021362	0.81[YRI][hapmap]
rs2101345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240332	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240333	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467590	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835295	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6537416	0.94[EUR][1000 genomes]
rs6823006	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6840788	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7689088	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7691153	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13147611	TTC29	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147174400-147231200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:147180400-147233200	Weak transcription	Liver	Liver
3	chr4:147201000-147249600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:147208200-147232800	Weak transcription	Aorta	Aorta
5	chr4:147208200-147234200	Weak transcription	Lung	lung
6	chr4:147208200-147247000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:147208400-147249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:147208400-147254600	Weak transcription	Gastric	stomach
9	chr4:147208600-147254800	Weak transcription	Adipose Nuclei	Adipose
10	chr4:147209200-147249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:147209400-147245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:147215600-147254800	Weak transcription	Primary T cells from cord blood	blood
14	chr4:147222800-147235800	Weak transcription	Esophagus	oesophagus
15	chr4:147224200-147235200	Weak transcription	Psoas Muscle	Psoas
16	chr4:147225600-147245600	Weak transcription	Primary B cells from cord blood	blood
17	chr4:147228200-147232000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:147228400-147235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:147229400-147231800	Weak transcription	NH-A	brain
20	chr4:147229600-147257400	Weak transcription	Ovary	ovary
21	chr4:147230600-147231200	Enhancers	GM12878-XiMat	blood
22	chr4:147230800-147244000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:147230800-147245600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:147231000-147232200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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