Variant report

Variant	rs7729287
Chromosome Location	chr5:178488991-178488992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178488576..178490984-chr5:178494204..178495758,2	MCF-7	breast:
2	chr5:178483141..178486203-chr5:178488375..178491712,3	MCF-7	breast:
3	chr5:178487796..178490140-chr5:178490313..178493225,2	MCF-7	breast:
4	chr5:178488531..178490916-chr5:178493267..178496128,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10073008	1.00[EUR][1000 genomes]
rs13357876	1.00[EUR][1000 genomes]
rs17078961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6601008	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6601009	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863623	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6863664	1.00[EUR][1000 genomes]
rs6886245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73342567	0.83[EUR][1000 genomes]
rs7733356	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178486600-178489000	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:178487000-178490000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:178487000-178497600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr5:178487800-178490200	ZNF genes & repeats	Fetal Thymus	thymus
5	chr5:178488000-178489200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr5:178488000-178489400	Weak transcription	Aorta	Aorta
7	chr5:178488000-178491000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:178488000-178493000	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr5:178488200-178489000	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:178488200-178489000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:178488200-178489000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:178488200-178489000	Enhancers	Placenta	Placenta
13	chr5:178488200-178489200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:178488200-178489200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:178488200-178491000	Weak transcription	Small Intestine	intestine
16	chr5:178488200-178491200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:178488200-178491200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
18	chr5:178488200-178493200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:178488200-178493200	ZNF genes & repeats	Fetal Stomach	stomach
20	chr5:178488200-178511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:178488400-178489000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr5:178488400-178489000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:178488400-178489000	Enhancers	Psoas Muscle	Psoas
24	chr5:178488400-178489000	ZNF genes & repeats	Thymus	Thymus
25	chr5:178488400-178489200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:178488400-178489200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr5:178488400-178489200	Weak transcription	Fetal Intestine Large	intestine
28	chr5:178488400-178489200	Enhancers	Spleen	Spleen
29	chr5:178488400-178489400	ZNF genes & repeats	NHDF-Ad	bronchial
30	chr5:178488400-178489600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:178488400-178489600	ZNF genes & repeats	HSMM	muscle
32	chr5:178488400-178489800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:178488400-178489800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:178488400-178491200	ZNF genes & repeats	NHLF	lung
35	chr5:178488400-178492200	Strong transcription	Fetal Lung	lung
36	chr5:178488400-178492400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:178488400-178492600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:178488400-178492800	Weak transcription	HUVEC	blood vessel
39	chr5:178488400-178492800	Weak transcription	NHEK	skin
40	chr5:178488400-178497400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
41	chr5:178488400-178497800	ZNF genes & repeats	Brain Germinal Matrix	brain
42	chr5:178488400-178499000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:178488400-178508400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr5:178488400-178511600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:178488400-178512000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:178488600-178489000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:178488600-178489000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr5:178488600-178489000	Enhancers	Brain Cingulate Gyrus	brain
49	chr5:178488600-178489000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr5:178488600-178489200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin

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