Variant report

Variant	rs298628
Chromosome Location	chr5:60452888-60452889
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	chr5:60450120..60453584-chr5:60455423..60459976,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10044518	1.00[JPT][hapmap]
rs10044575	1.00[JPT][hapmap]
rs12186613	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188621	1.00[JPT][hapmap]
rs12188882	1.00[JPT][hapmap]
rs159373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159540	0.88[ASN][1000 genomes]
rs167190	0.96[EUR][1000 genomes]
rs1841504	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295538	0.88[EUR][1000 genomes]
rs295547	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295548	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295549	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295550	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs295568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295574	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298625	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256302	1.00[JPT][hapmap]
rs498497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60436000-60457600	Weak transcription	Esophagus	oesophagus
3	chr5:60438000-60455400	Weak transcription	Fetal Brain Female	brain
4	chr5:60438600-60455600	Weak transcription	Fetal Kidney	kidney
5	chr5:60438800-60455800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:60440400-60457400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:60440600-60455800	Weak transcription	Left Ventricle	heart
8	chr5:60441000-60455800	Weak transcription	Pancreas	Pancrea
9	chr5:60442400-60455800	Weak transcription	NHLF	lung
10	chr5:60445400-60455000	Weak transcription	Fetal Lung	lung
11	chr5:60445600-60455600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:60446200-60454600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:60446600-60457400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:60446800-60456600	Weak transcription	Fetal Stomach	stomach
15	chr5:60447400-60457400	Weak transcription	Ovary	ovary
16	chr5:60448200-60453600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:60448200-60453800	Weak transcription	NH-A	brain
18	chr5:60448200-60454200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:60449000-60457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:60449200-60455400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:60449600-60454200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:60449800-60454400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:60450000-60455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:60450000-60457400	Weak transcription	Right Ventricle	heart
25	chr5:60450200-60455000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:60450200-60455600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:60450400-60457600	Weak transcription	Lung	lung
28	chr5:60450600-60454000	Weak transcription	Osteobl	bone
29	chr5:60450600-60455600	Weak transcription	Fetal Intestine Large	intestine
30	chr5:60450800-60456400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:60451000-60453600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:60451000-60455000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:60451000-60455800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:60451000-60457200	Weak transcription	Thymus	Thymus
35	chr5:60451200-60453400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:60451200-60455800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:60451200-60456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:60451400-60453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:60451400-60454600	Weak transcription	Hela-S3	cervix
40	chr5:60451400-60457000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:60451600-60453800	Weak transcription	HepG2	liver
42	chr5:60451600-60454000	Weak transcription	HMEC	breast
43	chr5:60451600-60455800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:60451600-60456400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:60451800-60453000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:60451800-60454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:60451800-60457600	Weak transcription	Spleen	Spleen
48	chr5:60452000-60453000	Strong transcription	Primary B cells from cord blood	blood
49	chr5:60452000-60453000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:60452000-60453400	Strong transcription	Fetal Muscle Trunk	muscle

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