Variant report

Variant	rs6889338
Chromosome Location	chr5:60589021-60589022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60588266..60590443-chr5:60596275..60598423,2	MCF-7	breast:
3	chr5:60586331..60590191-chr5:60626187..60629992,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10939897	0.84[CEU][hapmap]
rs11747144	0.86[CEU][hapmap]
rs13154663	0.81[CEU][hapmap]
rs13162866	0.88[CEU][hapmap]
rs13164720	0.88[CEU][hapmap]
rs13182603	0.82[EUR][1000 genomes]
rs4235486	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4391122	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4421060	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4513641	0.87[CEU][hapmap]
rs4544785	0.81[CEU][hapmap]
rs4546329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4583848	0.86[ASN][1000 genomes]
rs6449525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449526	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449527	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6860599	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6867278	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6870349	0.81[CEU][hapmap]
rs7444792	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
2	chr5:60585400-60589400	Enhancers	Pancreas	Pancrea
3	chr5:60586400-60589600	Enhancers	Stomach Mucosa	stomach
4	chr5:60586600-60589400	Enhancers	Duodenum Mucosa	Duodenum
5	chr5:60586600-60589400	Enhancers	Fetal Intestine Large	intestine
6	chr5:60586600-60590400	Enhancers	Fetal Intestine Small	intestine
7	chr5:60587000-60594000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60587000-60594600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:60587000-60595200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:60587000-60597400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:60587200-60593800	Weak transcription	A549	lung
12	chr5:60587200-60594000	Weak transcription	NHDF-Ad	bronchial
13	chr5:60587200-60595000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:60587200-60597200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:60587200-60597400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:60587400-60591800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:60587400-60591800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:60587400-60594200	Weak transcription	Osteobl	bone
19	chr5:60587400-60594400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:60587400-60594600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:60587400-60595200	Weak transcription	HSMM	muscle
22	chr5:60587600-60591600	Weak transcription	NHLF	lung
23	chr5:60588200-60589200	Enhancers	Adipose Nuclei	Adipose
24	chr5:60588200-60589200	Weak transcription	Fetal Kidney	kidney
25	chr5:60588200-60591400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:60588600-60589200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:60588600-60589800	Enhancers	Hela-S3	cervix
28	chr5:60588800-60589200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:60588800-60589200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:60588800-60589200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:60588800-60589200	Enhancers	Colonic Mucosa	Colon
32	chr5:60588800-60589200	Enhancers	Esophagus	oesophagus
33	chr5:60588800-60589200	Enhancers	Gastric	stomach
34	chr5:60588800-60589200	Enhancers	Lung	lung
35	chr5:60588800-60589200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr5:60588800-60589200	Bivalent Enhancer	Psoas Muscle	Psoas
37	chr5:60588800-60589200	Enhancers	NHEK	skin
38	chr5:60588800-60589400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:60588800-60589400	Enhancers	Brain Anterior Caudate	brain
40	chr5:60588800-60589400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr5:60588800-60589400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr5:60588800-60589800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr5:60589000-60589200	Enhancers	Ovary	ovary

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