Variant report

Variant	rs3857434
Chromosome Location	chr5:112365804-112365805
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	chr5:112363970..112366861-chr5:112379639..112381179,2	K562	blood:
2	chr5:112365166..112368140-chr5:112517224..112519156,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10039618	0.80[JPT][hapmap]
rs10054158	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs1057474	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11749921	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12517398	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12654474	0.82[EUR][1000 genomes]
rs13156493	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs13159449	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13171553	0.81[EUR][1000 genomes]
rs13177101	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs13186334	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13445	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1363333	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549181	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17312754	0.83[EUR][1000 genomes]
rs17372511	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112454	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs2227948	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416300	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3185733	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33544	0.90[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs33551	0.86[JPT][hapmap]
rs33552	0.81[JPT][hapmap]
rs33554	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs33557	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs33568	0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs33569	0.80[CHB][hapmap]
rs4073358	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073359	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074190	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4075350	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4301226	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs4428399	0.83[ASN][1000 genomes]
rs4599529	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs4705529	0.86[EUR][1000 genomes]
rs4705744	0.89[EUR][1000 genomes]
rs4705745	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705749	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705750	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705752	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705755	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705756	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705758	0.85[JPT][hapmap]
rs4705762	0.84[AMR][1000 genomes]
rs4778	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6594665	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs6869100	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6877769	0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6890872	0.81[MKK][hapmap]
rs6893016	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[AMR][1000 genomes]
rs6893389	0.81[JPT][hapmap]
rs6894219	0.90[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6894937	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7670	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7701781	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7732198	0.81[JPT][hapmap]
rs9122	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9784647	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3857434	MCC	cis	Whole Blood	GTEx
rs3857434	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs3857434	DCP2	cis	multi-tissue	Pritchard
rs3857434	DCP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
4	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:112352400-112367800	Strong transcription	Liver	Liver
6	chr5:112358800-112366000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:112359600-112367800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
9	chr5:112360200-112368600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:112360400-112367200	Weak transcription	GM12878-XiMat	blood
11	chr5:112360400-112367600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:112360400-112368000	Weak transcription	Primary B cells from cord blood	blood
13	chr5:112360400-112368400	Weak transcription	Stomach Mucosa	stomach
14	chr5:112361000-112368000	Strong transcription	Fetal Stomach	stomach
15	chr5:112361400-112366200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:112361400-112367400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:112361400-112368200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:112361800-112366000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:112363000-112374000	Weak transcription	Pancreas	Pancrea
21	chr5:112363200-112366200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:112363600-112366000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:112363600-112366200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:112363600-112368400	Weak transcription	Psoas Muscle	Psoas
25	chr5:112363600-112368600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:112363600-112379000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:112363600-112379000	Weak transcription	Brain Substantia Nigra	brain
28	chr5:112363600-112379200	Weak transcription	Gastric	stomach
29	chr5:112363600-112379200	Weak transcription	Spleen	Spleen
30	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
31	chr5:112363800-112368200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:112363800-112371000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:112363800-112372000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:112363800-112372200	Weak transcription	Fetal Brain Female	brain
35	chr5:112363800-112376200	Weak transcription	Dnd41	blood
36	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
37	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
40	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:112364000-112367200	Weak transcription	Brain Germinal Matrix	brain
42	chr5:112364000-112367200	Weak transcription	K562	blood
43	chr5:112364000-112367800	Weak transcription	Brain Anterior Caudate	brain
44	chr5:112364000-112368400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:112364000-112368600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:112364000-112368600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:112364000-112370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:112364000-112374200	Weak transcription	HUVEC	blood vessel
49	chr5:112364000-112374600	Weak transcription	Lung	lung
50	chr5:112364000-112379000	Weak transcription	Fetal Lung	lung

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