Variant report

Variant	rs6594665
Chromosome Location	chr5:112388225-112388226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112381725..112385379-chr5:112386016..112389315,3	MCF-7	breast:
2	chr5:112387805..112389786-chr5:112405042..112406689,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10039618	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10054158	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10477486	0.90[CHB][hapmap]
rs10478102	0.81[CHB][hapmap]
rs1057474	0.85[JPT][hapmap]
rs11749921	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13156493	0.82[JPT][hapmap]
rs13177101	0.81[JPT][hapmap]
rs13186334	0.81[JPT][hapmap]
rs1363333	0.85[JPT][hapmap]
rs1549181	0.85[JPT][hapmap]
rs17372511	0.80[JPT][hapmap]
rs2227947	0.90[CHB][hapmap]
rs2227948	0.89[ASN][1000 genomes]
rs2416300	0.83[JPT][hapmap]
rs3185733	0.81[JPT][hapmap]
rs33557	0.81[JPT][hapmap]
rs3857434	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs4073358	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4073359	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4074190	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4075350	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs4235788	0.89[CHB][hapmap]
rs4301226	0.89[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4428399	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4463174	0.90[CHB][hapmap]
rs4599529	0.84[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4705750	0.85[JPT][hapmap]
rs4705752	0.85[JPT][hapmap]
rs4705755	0.89[ASN][1000 genomes]
rs4705756	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4705758	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4705762	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705763	0.97[ASN][1000 genomes]
rs4705767	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4778	0.81[JPT][hapmap]
rs6862481	0.89[CHB][hapmap]
rs6877769	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6879633	0.81[CHB][hapmap]
rs6893016	0.84[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6893389	0.95[JPT][hapmap]
rs6894219	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6894937	0.93[ASN][1000 genomes]
rs71590730	0.82[AFR][1000 genomes]
rs7701781	0.85[JPT][hapmap]
rs7708603	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7730767	0.90[CHB][hapmap]
rs7731890	0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.87[ASN][1000 genomes]
rs7732198	0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs9122	0.85[JPT][hapmap]
rs9784647	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv516887	chr5:112379659-112396174	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
3	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
14	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
15	chr5:112379600-112388800	Weak transcription	Gastric	stomach
16	chr5:112379600-112388800	Weak transcription	Spleen	Spleen
17	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
19	chr5:112379800-112388800	Weak transcription	Brain Substantia Nigra	brain
20	chr5:112383200-112409400	Strong transcription	Liver	Liver
21	chr5:112383400-112395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:112383600-112392000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:112383600-112394200	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:112383800-112389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:112383800-112393000	Weak transcription	Brain Germinal Matrix	brain
26	chr5:112383800-112394000	Weak transcription	Fetal Thymus	thymus
27	chr5:112384000-112388400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:112384000-112389800	Enhancers	K562	blood
29	chr5:112384000-112393200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:112384200-112388400	Weak transcription	Fetal Intestine Small	intestine
32	chr5:112384200-112390200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:112384200-112392600	Weak transcription	Fetal Kidney	kidney
34	chr5:112384200-112393000	Weak transcription	Fetal Brain Male	brain
35	chr5:112384200-112411000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:112384600-112398400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:112384600-112398800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:112384800-112399000	Weak transcription	Aorta	Aorta
39	chr5:112385000-112389200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:112385000-112390400	Weak transcription	Lung	lung
41	chr5:112385600-112388800	Weak transcription	Fetal Lung	lung
42	chr5:112385800-112388600	Enhancers	HMEC	breast
43	chr5:112385800-112389000	Enhancers	Right Atrium	heart
44	chr5:112386000-112388600	Enhancers	NHDF-Ad	bronchial
45	chr5:112386000-112388800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:112386000-112389000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:112386000-112397200	Weak transcription	Fetal Heart	heart
48	chr5:112386200-112388600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr5:112386200-112388600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:112386200-112388600	Enhancers	HSMM	muscle

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