Variant report

Variant	rs888844
Chromosome Location	chr5:112371641-112371642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112370113..112371972-chr5:112381574..112383609,2	MCF-7	breast:
2	chr5:112361859..112364300-chr5:112370845..112373439,3	K562	blood:
3	chr5:112312938..112314772-chr5:112369842..112371988,2	K562	blood:
4	chr5:112368998..112372284-chr5:112372465..112374362,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10059599	1.00[JPT][hapmap]
rs12516502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12719155	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2052484	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2080896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080897	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2112452	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2112453	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161244	0.98[ASN][1000 genomes]
rs2416301	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33550	0.91[JPT][hapmap]
rs33553	0.91[JPT][hapmap]
rs33563	0.91[JPT][hapmap]
rs33565	0.91[JPT][hapmap]
rs3733969	1.00[JPT][hapmap]
rs3857433	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4260660	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4705530	1.00[JPT][hapmap]
rs4705532	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4705533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4705743	1.00[JPT][hapmap]
rs4705746	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4705751	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4705754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs59147465	0.82[EUR][1000 genomes]
rs59265685	0.82[EUR][1000 genomes]
rs6594659	0.93[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6594660	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6594662	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7447818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7718810	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7721666	0.85[EUR][1000 genomes]
rs878073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs878076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs882253	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888845	0.98[ASN][1000 genomes]
rs9326869	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs959949	1.00[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs888844	DCP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
2	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
3	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:112363000-112374000	Weak transcription	Pancreas	Pancrea
5	chr5:112363600-112379000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:112363600-112379000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:112363600-112379200	Weak transcription	Gastric	stomach
8	chr5:112363600-112379200	Weak transcription	Spleen	Spleen
9	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
10	chr5:112363800-112372000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:112363800-112372200	Weak transcription	Fetal Brain Female	brain
12	chr5:112363800-112376200	Weak transcription	Dnd41	blood
13	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
14	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
17	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:112364000-112374200	Weak transcription	HUVEC	blood vessel
19	chr5:112364000-112374600	Weak transcription	Lung	lung
20	chr5:112364000-112379000	Weak transcription	Fetal Lung	lung
21	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:112364600-112372200	Weak transcription	Fetal Kidney	kidney
24	chr5:112364600-112379000	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:112364800-112378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:112364800-112382800	Weak transcription	Fetal Intestine Large	intestine
27	chr5:112364800-112382800	Weak transcription	Fetal Thymus	thymus
28	chr5:112365400-112372000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:112365600-112372000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:112365600-112376400	Weak transcription	Primary T cells from cord blood	blood
31	chr5:112365800-112372000	Weak transcription	Esophagus	oesophagus
32	chr5:112365800-112376800	Weak transcription	Thymus	Thymus
33	chr5:112365800-112382200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:112366000-112371800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:112366600-112379200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:112367600-112372200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:112367600-112372200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:112367600-112372200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:112367600-112378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:112367800-112372000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:112368800-112379400	Strong transcription	Fetal Stomach	stomach
42	chr5:112368800-112382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:112369000-112372000	Weak transcription	Left Ventricle	heart
44	chr5:112369000-112379000	Weak transcription	Psoas Muscle	Psoas
45	chr5:112369200-112378800	Weak transcription	Fetal Heart	heart
46	chr5:112369200-112380200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:112369400-112377400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:112369400-112382800	Strong transcription	Liver	Liver
49	chr5:112369800-112378000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:112370200-112379200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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