Variant report

Variant	rs10939898
Chromosome Location	chr5:60612602-60612603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60611558..60614120-chr5:60615826..60618466,2	MCF-7	breast:
2	chr5:60603025..60605964-chr5:60611139..60612666,2	MCF-7	breast:
3	chr5:60609834..60612725-chr5:60612817..60615641,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10939897	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11743133	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11747144	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11960587	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13154581	0.86[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13154663	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13156118	0.86[CEU][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13162866	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164720	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171223	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13174916	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13182603	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34323293	0.81[EUR][1000 genomes]
rs4409043	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4513641	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4544785	0.93[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62366236	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6449526	0.93[CEU][hapmap]
rs6449527	0.87[CEU][hapmap]
rs6860599	0.93[CEU][hapmap]
rs6867278	0.87[CEU][hapmap]
rs6870349	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6881622	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6889338	0.87[CEU][hapmap]
rs7704636	0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	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
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60600800-60615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:60607800-60614600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:60608800-60614400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:60608800-60615400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:60610000-60614000	Weak transcription	Lung	lung
6	chr5:60610000-60618600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:60610200-60613400	Weak transcription	Brain Anterior Caudate	brain
8	chr5:60610200-60613400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:60610200-60614000	Weak transcription	Adipose Nuclei	Adipose
10	chr5:60610200-60614800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:60610200-60615000	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:60610400-60613400	Weak transcription	Fetal Lung	lung
13	chr5:60610400-60614600	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:60610400-60614600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:60610400-60614800	Weak transcription	Small Intestine	intestine
16	chr5:60610400-60615000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:60610400-60615000	Weak transcription	Stomach Mucosa	stomach
18	chr5:60610400-60615400	Weak transcription	Placenta	Placenta
19	chr5:60610800-60613600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr5:60610800-60614200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:60610800-60614400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:60610800-60615000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:60610800-60618600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:60611000-60613400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:60611000-60613800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:60611000-60614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:60611000-60614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:60611000-60614800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:60611000-60615200	Weak transcription	NHEK	skin
30	chr5:60611000-60615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:60611200-60614000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:60611200-60618200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:60611400-60614000	Weak transcription	NHDF-Ad	bronchial
34	chr5:60611400-60614000	Weak transcription	Osteobl	bone
35	chr5:60611400-60615000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:60611400-60618200	Weak transcription	NH-A	brain
37	chr5:60611400-60618800	Weak transcription	A549	lung
38	chr5:60611600-60614000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:60611600-60614000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:60611600-60614000	Weak transcription	HSMMtube	muscle
41	chr5:60611800-60613400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:60611800-60613400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:60611800-60613800	Weak transcription	HUVEC	blood vessel
44	chr5:60611800-60615400	Weak transcription	NHLF	lung
45	chr5:60611800-60618400	Weak transcription	HSMM	muscle

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