Variant report

Variant	rs6594659
Chromosome Location	chr5:112374562-112374563
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112373432..112375747-chr5:112376830..112379641,2	K562	blood:
2	chr5:112372883..112375761-chr5:112416823..112419304,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10059599	0.94[JPT][hapmap]
rs12516502	0.94[JPT][hapmap]
rs12719155	0.85[JPT][hapmap]
rs2052484	0.94[JPT][hapmap];0.80[MEX][hapmap]
rs2080896	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2112452	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs2112453	0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2416301	0.85[EUR][1000 genomes]
rs33550	0.88[JPT][hapmap]
rs33553	0.88[JPT][hapmap]
rs33563	0.88[JPT][hapmap]
rs33565	0.88[JPT][hapmap]
rs3733969	0.80[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs3857433	0.80[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs4260660	0.88[JPT][hapmap]
rs4705530	0.94[JPT][hapmap]
rs4705533	0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs4705743	0.94[JPT][hapmap]
rs4705754	0.93[JPT][hapmap]
rs59147465	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59265685	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59664033	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594660	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594662	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892724	0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7447818	0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs7718810	0.94[JPT][hapmap]
rs7721666	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs878073	0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs878076	0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs882253	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs888844	0.93[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9326869	0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs959949	0.88[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6594659	MCC	cis	parietal	SCAN
rs6594659	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
2	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:112363600-112379000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:112363600-112379000	Weak transcription	Brain Substantia Nigra	brain
5	chr5:112363600-112379200	Weak transcription	Gastric	stomach
6	chr5:112363600-112379200	Weak transcription	Spleen	Spleen
7	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:112363800-112376200	Weak transcription	Dnd41	blood
9	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
10	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
13	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:112364000-112374600	Weak transcription	Lung	lung
15	chr5:112364000-112379000	Weak transcription	Fetal Lung	lung
16	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:112364600-112379000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:112364800-112378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:112364800-112382800	Weak transcription	Fetal Intestine Large	intestine
21	chr5:112364800-112382800	Weak transcription	Fetal Thymus	thymus
22	chr5:112365600-112376400	Weak transcription	Primary T cells from cord blood	blood
23	chr5:112365800-112376800	Weak transcription	Thymus	Thymus
24	chr5:112365800-112382200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:112366600-112379200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:112367600-112378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:112368800-112379400	Strong transcription	Fetal Stomach	stomach
28	chr5:112368800-112382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:112369000-112379000	Weak transcription	Psoas Muscle	Psoas
30	chr5:112369200-112378800	Weak transcription	Fetal Heart	heart
31	chr5:112369200-112380200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112369400-112377400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:112369400-112382800	Strong transcription	Liver	Liver
34	chr5:112369800-112378000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:112370200-112379200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:112370600-112382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:112371000-112383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:112371200-112378600	Weak transcription	Right Atrium	heart
41	chr5:112371400-112379000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:112371400-112382600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:112371600-112376000	Strong transcription	Adipose Nuclei	Adipose
46	chr5:112371600-112379000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:112372000-112376200	Strong transcription	Esophagus	oesophagus
49	chr5:112372200-112374600	Strong transcription	Fetal Kidney	kidney
50	chr5:112372600-112384000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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