Variant report

Variant	rs6861939
Chromosome Location	chr5:112597766-112597767
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112595001..112597211-chr5:112597744..112599489,3	MCF-7	breast:
2	chr5:112597661..112600348-chr5:112601306..112603277,2	MCF-7	breast:
3	chr5:112566555..112568778-chr5:112596838..112599414,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10519342	0.88[YRI][hapmap]
rs10519348	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10519354	1.00[CHB][hapmap]
rs11739509	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11740807	0.87[EUR][1000 genomes]
rs11741176	0.88[EUR][1000 genomes]
rs11750752	0.87[EUR][1000 genomes]
rs13162970	1.00[JPT][hapmap]
rs13177178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13182359	1.00[JPT][hapmap]
rs1318772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13188803	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs164252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17325908	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17326496	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17327139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2091802	1.00[YRI][hapmap]
rs2120348	1.00[CHB][hapmap]
rs255857	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26965	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26982	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26984	1.00[JPT][hapmap]
rs26989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26990	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34441430	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34614757	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34766128	0.97[EUR][1000 genomes]
rs35352601	0.87[EUR][1000 genomes]
rs36120874	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36611	1.00[JPT][hapmap]
rs36613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66957398	0.88[EUR][1000 genomes]
rs67894881	0.84[ASN][1000 genomes]
rs6879776	0.85[YRI][hapmap]
rs72788641	0.84[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112582800-112601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:112583600-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112586600-112598800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
6	chr5:112586800-112598800	Weak transcription	Fetal Kidney	kidney
7	chr5:112586800-112599400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:112587200-112599400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:112588000-112598600	Weak transcription	Fetal Lung	lung
11	chr5:112588000-112601200	Weak transcription	HMEC	breast
12	chr5:112589200-112610600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:112589400-112602200	Weak transcription	Esophagus	oesophagus
14	chr5:112591600-112598400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:112591600-112602000	Weak transcription	Brain Substantia Nigra	brain
16	chr5:112593600-112599400	Weak transcription	Fetal Heart	heart
17	chr5:112593800-112598800	Weak transcription	Liver	Liver
18	chr5:112593800-112599800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:112594200-112597800	Weak transcription	Right Atrium	heart
20	chr5:112594400-112598000	Weak transcription	Ovary	ovary
21	chr5:112594400-112602200	Weak transcription	Left Ventricle	heart
22	chr5:112594400-112602200	Weak transcription	Right Ventricle	heart
23	chr5:112595200-112600800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:112595200-112601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112595400-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:112595600-112599200	Weak transcription	NHEK	skin
27	chr5:112595600-112602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:112597000-112599800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:112597000-112600800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:112597200-112598800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:112597400-112598200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:112597600-112598800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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