Variant report

Variant	rs12652099
Chromosome Location	chr5:177856652-177856653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177851066..177853109-chr5:177854719..177857640,2	MCF-7	breast:
2	chr5:177855622..177857824-chr5:177858602..177861991,3	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17081213	0.81[CHB][hapmap]
rs17081217	0.81[CHB][hapmap]
rs17081220	0.81[CHB][hapmap]
rs17081256	1.00[CEU][hapmap]
rs17081260	1.00[CEU][hapmap]
rs4618447	1.00[CEU][hapmap]
rs6601235	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs6868772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6886832	1.00[CEU][hapmap]
rs6896228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72648834	0.81[AMR][1000 genomes]
rs7726125	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7728076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
2	chr5:177853000-177857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:177854200-177857600	Enhancers	Fetal Lung	lung
5	chr5:177854400-177856800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:177854400-177856800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:177854400-177857200	Enhancers	Fetal Stomach	stomach
8	chr5:177854400-177857400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:177855000-177856800	Enhancers	Brain Anterior Caudate	brain
10	chr5:177855000-177856800	Enhancers	Brain Hippocampus Middle	brain
11	chr5:177855000-177856800	Enhancers	Left Ventricle	heart
12	chr5:177855000-177857000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:177855000-177857000	Enhancers	Psoas Muscle	Psoas
14	chr5:177855000-177857200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr5:177855000-177857200	Enhancers	Placenta	Placenta
16	chr5:177855000-177857200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr5:177855200-177856800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:177855200-177856800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:177855200-177857000	Enhancers	Spleen	Spleen
20	chr5:177855200-177857200	Enhancers	Liver	Liver
21	chr5:177855200-177857200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr5:177855200-177857200	Enhancers	Lung	lung
23	chr5:177855400-177857200	Enhancers	Esophagus	oesophagus
24	chr5:177855600-177856800	Enhancers	Fetal Heart	heart
25	chr5:177855600-177856800	Enhancers	Right Atrium	heart
26	chr5:177855600-177858200	Enhancers	Pancreas	Pancrea
27	chr5:177855800-177857000	Enhancers	Right Ventricle	heart
28	chr5:177855800-177857600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:177856000-177857000	Enhancers	Gastric	stomach
30	chr5:177856000-177861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:177856200-177857200	Genic enhancers	Fetal Thymus	thymus
32	chr5:177856400-177856800	Enhancers	Brain Angular Gyrus	brain
33	chr5:177856400-177856800	Active TSS	Fetal Brain Male	brain
34	chr5:177856400-177857000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:177856400-177857000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:177856400-177857000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:177856400-177857200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:177856400-177857200	Enhancers	Fetal Kidney	kidney
39	chr5:177856400-177857600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr5:177856400-177857600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr5:177856400-177861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:177856600-177857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:177856600-177861000	Weak transcription	Brain Cingulate Gyrus	brain

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