Variant report

Variant	rs4599529
Chromosome Location	chr5:112385447-112385448
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	chr5:112384421..112386665-chr5:112391243..112394084,2	MCF-7	breast:
2	chr5:112384021..112386512-chr5:112388336..112390508,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10039618	0.80[CHB][hapmap]
rs10054158	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10477486	0.85[CHB][hapmap]
rs11749921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1363333	0.82[GIH][hapmap]
rs2227947	0.85[CHB][hapmap]
rs2227948	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3857434	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs4073358	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073359	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4074190	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075350	0.81[CHD][hapmap];0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs4235788	0.84[CHB][hapmap]
rs4301226	0.94[ASW][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap]
rs4428399	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4463174	0.85[CHB][hapmap]
rs4705750	0.86[GIH][hapmap]
rs4705752	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs4705755	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705756	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705758	0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705763	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705767	0.84[ASN][1000 genomes]
rs6594665	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]
rs6862481	0.84[CHB][hapmap]
rs6877570	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6877769	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6893016	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6893389	0.85[CHB][hapmap]
rs6894219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6894937	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71590730	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7708603	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730767	0.85[CHB][hapmap]
rs7731890	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732198	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4599529	MCC	cis	cerebellum	SCAN
rs4599529	TSLP	cis	parietal	SCAN
rs4599529	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs4599529	DCP2	cis	lymphoblastoid	seeQTL
rs4599529	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
5	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:112374800-112386000	Weak transcription	NHDF-Ad	bronchial
17	chr5:112374800-112386200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
19	chr5:112377400-112386400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
21	chr5:112379600-112386400	Weak transcription	Brain Angular Gyrus	brain
22	chr5:112379600-112386400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:112379600-112388800	Weak transcription	Gastric	stomach
24	chr5:112379600-112388800	Weak transcription	Spleen	Spleen
25	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
27	chr5:112379800-112386200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:112379800-112386400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:112379800-112388800	Weak transcription	Brain Substantia Nigra	brain
30	chr5:112381600-112385800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:112382600-112386200	Genic enhancers	Fetal Muscle Leg	muscle
32	chr5:112382600-112387200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:112382600-112387400	Enhancers	Placenta	Placenta
34	chr5:112382800-112386000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:112383000-112386000	Strong transcription	Right Ventricle	heart
36	chr5:112383200-112409400	Strong transcription	Liver	Liver
37	chr5:112383400-112385800	Strong transcription	Esophagus	oesophagus
38	chr5:112383400-112386200	Weak transcription	Osteobl	bone
39	chr5:112383400-112386400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:112383400-112386400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:112383400-112395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:112383600-112386000	Strong transcription	Fetal Heart	heart
43	chr5:112383600-112386200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:112383600-112386200	Weak transcription	HSMM	muscle
45	chr5:112383600-112392000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:112383600-112394200	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:112383800-112385600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr5:112383800-112385800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:112383800-112385800	Weak transcription	Right Atrium	heart
50	chr5:112383800-112386200	Weak transcription	Hela-S3	cervix

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