Variant report

Variant	rs57077871
Chromosome Location	chr5:112920871-112920872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112919623..112922323-chr5:112924895..112926616,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11747924	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11748145	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11748794	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12519323	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135753	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135754	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1833678	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2042222	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2195380	0.84[ASN][1000 genomes]
rs2288449	0.82[EUR][1000 genomes]
rs2416281	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815911	0.82[EUR][1000 genomes]
rs3846722	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4122546	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705551	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705557	0.82[EUR][1000 genomes]
rs4705558	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705826	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56206672	0.82[EUR][1000 genomes]
rs6594737	0.82[AMR][1000 genomes]
rs66490974	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66497221	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67020702	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67103739	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67723806	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6859688	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6861786	0.80[AMR][1000 genomes]
rs6864369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878001	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882900	0.80[EUR][1000 genomes]
rs6883441	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6884704	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6896469	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6896501	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72794121	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72805465	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73241779	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73242809	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73247445	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702833	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7707443	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7729433	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs957777	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882721	chr5:112859994-112963488	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv882724	chr5:112868878-112933202	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv1033202	chr5:112891857-112945992	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv520674	chr5:112911165-112942820	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv2752057	chr5:112916398-112945992	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1029507	chr5:112916398-112945992	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv2763910	chr5:112916398-112951827	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv1031336	chr5:112916398-112956588	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57077871	YTHDC2	cis	multi-tissue	Pritchard
rs57077871	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112867400-112926000	Weak transcription	Small Intestine	intestine
2	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:112898200-112921200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:112899400-112929400	Weak transcription	HepG2	liver
7	chr5:112904600-112934800	Weak transcription	Psoas Muscle	Psoas
8	chr5:112907400-112932000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:112908800-112935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:112910600-112927000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:112910600-112927600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:112910600-112927800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:112910600-112933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:112910600-112935200	Weak transcription	Spleen	Spleen
15	chr5:112910600-112935400	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:112910600-112936600	Weak transcription	Colonic Mucosa	Colon
17	chr5:112910600-112942000	Weak transcription	Brain Substantia Nigra	brain
18	chr5:112910800-112924400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:112910800-112927600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:112910800-112928400	Weak transcription	A549	lung
21	chr5:112910800-112928600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:112910800-112929200	Weak transcription	Right Ventricle	heart
23	chr5:112910800-112929400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:112910800-112930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:112910800-112933600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:112910800-112933600	Weak transcription	Fetal Stomach	stomach
27	chr5:112910800-112934600	Weak transcription	Gastric	stomach
28	chr5:112910800-112935000	Weak transcription	Pancreas	Pancrea
29	chr5:112910800-112935200	Weak transcription	Esophagus	oesophagus
30	chr5:112910800-112937400	Weak transcription	Fetal Intestine Small	intestine
31	chr5:112910800-112938200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:112910800-112942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:112911000-112930000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:112911200-112925400	Weak transcription	Brain Germinal Matrix	brain
35	chr5:112911200-112929000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:112914000-112922200	Strong transcription	Dnd41	blood
37	chr5:112915200-112922200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:112915200-112922200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:112915200-112922200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:112915400-112921400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:112916000-112931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:112916400-112926800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:112916400-112929200	Weak transcription	Lung	lung
44	chr5:112916400-112930400	Weak transcription	NHLF	lung
45	chr5:112916400-112933000	Weak transcription	Thymus	Thymus
46	chr5:112916400-112933400	Weak transcription	Aorta	Aorta
47	chr5:112916800-112928600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:112916800-112928600	Weak transcription	NH-A	brain
49	chr5:112916800-112936000	Weak transcription	Fetal Heart	heart
50	chr5:112917200-112926200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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