Variant report

Variant	rs1833678
Chromosome Location	chr5:112853189-112853190
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	chr5:112846816..112849385-chr5:112852983..112854896,2	MCF-7	breast:
2	chr5:112781329..112783390-chr5:112851064..112853901,2	K562	blood:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap]
rs10071816	0.94[CEU][hapmap]
rs10079895	0.94[CEU][hapmap]
rs10079973	0.94[CEU][hapmap]
rs10080096	0.89[CEU][hapmap]
rs10428666	1.00[JPT][hapmap]
rs10477497	0.88[CEU][hapmap]
rs10478127	0.94[CEU][hapmap]
rs10900685	0.86[JPT][hapmap]
rs1116547	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11241201	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11241206	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs11241214	0.94[CEU][hapmap]
rs11241215	0.88[CEU][hapmap]
rs11738075	1.00[JPT][hapmap]
rs11738215	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs11747924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748145	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11748794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap]
rs11956399	0.94[CEU][hapmap]
rs12186798	0.94[CEU][hapmap]
rs12514091	1.00[JPT][hapmap]
rs12516418	0.86[JPT][hapmap]
rs12519323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519818	0.81[ASN][1000 genomes]
rs12523255	1.00[JPT][hapmap]
rs12660001	0.94[CEU][hapmap]
rs1443683	1.00[JPT][hapmap]
rs17135597	1.00[JPT][hapmap]
rs17135608	1.00[JPT][hapmap]
rs17135616	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs17135630	0.86[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs17135753	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1850410	1.00[JPT][hapmap]
rs2042222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068923	1.00[JPT][hapmap]
rs2288449	0.94[CEU][hapmap]
rs2416281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3763140	0.94[CEU][hapmap]
rs3815911	0.94[CEU][hapmap]
rs3846721	0.86[ASW][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[YRI][hapmap]
rs3846722	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3936061	0.94[CEU][hapmap]
rs4122546	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4334877	0.88[CEU][hapmap]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705814	1.00[JPT][hapmap]
rs4705817	1.00[JPT][hapmap]
rs4705819	1.00[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57077871	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6594734	0.94[CEU][hapmap]
rs6594737	0.83[AMR][1000 genomes]
rs66490974	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66497221	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66502937	0.81[ASN][1000 genomes]
rs66583752	0.81[ASN][1000 genomes]
rs67020702	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67103739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67268709	0.81[ASN][1000 genomes]
rs67723806	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6859688	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6861786	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6864369	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6864528	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6877432	0.89[CEU][hapmap]
rs6877524	1.00[JPT][hapmap]
rs6878001	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6879800	0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs6882900	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs6883441	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6886628	0.94[CEU][hapmap]
rs6889574	0.94[CEU][hapmap]
rs6896469	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6896501	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6898425	0.81[CEU][hapmap]
rs72792179	0.81[ASN][1000 genomes]
rs72794121	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72805465	0.84[EUR][1000 genomes]
rs73241779	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73242809	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73247445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7349799	0.87[CEU][hapmap]
rs7702833	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706958	0.94[CEU][hapmap]
rs7707443	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap]
rs7711367	0.94[CEU][hapmap]
rs7717000	0.88[JPT][hapmap]
rs7729433	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7737023	0.94[CEU][hapmap]
rs919304	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs9326893	0.94[CEU][hapmap]
rs957777	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1833678	DCP2	cis	parietal	SCAN
rs1833678	YTHDC2	cis	multi-tissue	Pritchard
rs1833678	YTHDC2	cis	cerebellum	SCAN
rs1833678	YTHDC2	cis	parietal	SCAN
rs1833678	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112850400-112853200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr5:112850400-112853200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:112850400-112853400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr5:112850400-112855600	Weak transcription	Left Ventricle	heart
5	chr5:112850400-112856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112850400-112856200	Weak transcription	Ovary	ovary
7	chr5:112850400-112856200	Weak transcription	Thymus	Thymus
8	chr5:112850400-112857800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:112850400-112858200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:112850400-112863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:112850400-112866600	Weak transcription	Esophagus	oesophagus
12	chr5:112850400-112866600	Weak transcription	Placenta	Placenta
13	chr5:112850400-112866800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:112850400-112866800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:112850400-112866800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:112850400-112866800	Weak transcription	Aorta	Aorta
17	chr5:112850400-112866800	Weak transcription	Lung	lung
18	chr5:112850400-112867000	Weak transcription	Pancreas	Pancrea
19	chr5:112850400-112879000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:112850400-112879200	Weak transcription	Gastric	stomach
21	chr5:112850400-112904000	Weak transcription	Psoas Muscle	Psoas
22	chr5:112850600-112853400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:112850600-112853800	Weak transcription	Fetal Stomach	stomach
24	chr5:112850600-112855200	Weak transcription	Right Ventricle	heart
25	chr5:112850600-112857600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:112850600-112860600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:112850600-112862000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:112850600-112865400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112850600-112865600	Weak transcription	Fetal Kidney	kidney
30	chr5:112850600-112866600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:112850600-112866600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:112850600-112867600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:112850600-112868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:112850600-112874800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:112850600-112879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
37	chr5:112850800-112853600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:112850800-112853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:112850800-112854200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:112850800-112856200	Weak transcription	NHDF-Ad	bronchial
41	chr5:112850800-112856400	Weak transcription	Brain Germinal Matrix	brain
42	chr5:112851200-112853400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:112851200-112856200	Weak transcription	HMEC	breast
44	chr5:112851200-112856800	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:112851200-112857000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr5:112851200-112858200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:112851400-112853200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:112851400-112853200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr5:112851400-112855800	Weak transcription	NHEK	skin
50	chr5:112851400-112856600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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