Variant report

Variant	rs4835295
Chromosome Location	chr4:147248896-147248897
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	chr4:147246661..147249612-chr4:147255793..147257750,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10011474	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10012369	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212750	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10213552	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]
rs13107111	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13121171	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13147611	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]
rs2101345	1.00[CEU][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4240332	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4240333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4467590	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4835293	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6537416	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6823006	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6840788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7691153	0.90[CEU][hapmap]

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	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
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4835295	TTC29	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147201000-147249600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:147208400-147249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:147208400-147254600	Weak transcription	Gastric	stomach
4	chr4:147208600-147254800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:147209200-147249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:147215600-147254800	Weak transcription	Primary T cells from cord blood	blood
8	chr4:147229600-147257400	Weak transcription	Ovary	ovary
9	chr4:147233000-147255000	Weak transcription	Aorta	Aorta
10	chr4:147233200-147254400	Weak transcription	GM12878-XiMat	blood
11	chr4:147234600-147249000	Weak transcription	Lung	lung
12	chr4:147235200-147249600	Weak transcription	Left Ventricle	heart
13	chr4:147241800-147255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:147242800-147255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:147243000-147255000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:147243200-147254800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:147244000-147251000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:147244200-147255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:147244600-147249600	Weak transcription	NH-A	brain
21	chr4:147245200-147249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:147245200-147249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:147245800-147249200	Weak transcription	HSMM	muscle
24	chr4:147245800-147249400	Weak transcription	HSMMtube	muscle
25	chr4:147246200-147249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:147246200-147249600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:147246200-147254800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:147246200-147255000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:147246400-147254000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:147246800-147249800	Weak transcription	Liver	Liver
31	chr4:147247600-147255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:147248400-147249400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:147248800-147250200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:147248800-147252400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:147248800-147257200	Weak transcription	Fetal Intestine Large	intestine

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