Variant report

Variant	rs2319887
Chromosome Location	chr4:69208309-69208310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:69206551-69208359	K562	blood:	n/a	n/a
2	POLR2A	chr4:69207877-69208530	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:69208126-69208450	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:69197134..69202591-chr4:69207411..69211710,5	K562	blood:
2	chr4:69188491..69190589-chr4:69207832..69210150,2	K562	blood:
3	chr4:69208163..69209683-chr4:69233967..69235522,2	MCF-7	breast:
4	chr4:69193259..69194902-chr4:69207176..69209237,2	K562	blood:
5	chr4:69201801..69210708-chr4:69210917..69216982,18	MCF-7	breast:

Variant related genes	Relation type
YTHDC1	TF binding region
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10005832	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10471153	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10866204	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11131746	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11732554	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11735530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12331971	0.83[ASN][1000 genomes]
rs13121372	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13127027	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13148330	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1320797	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406695	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1406696	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17089240	0.95[CEU][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17089241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1715086	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1730872	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1730875	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880183	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962172	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2140519	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34032921	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34186169	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34223548	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34265565	0.91[EUR][1000 genomes]
rs34282559	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34474886	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34527218	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34896019	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35051311	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797007	0.82[ASN][1000 genomes]
rs3927373	0.95[ASN][1000 genomes]
rs4860292	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860927	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860928	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860930	0.87[ASN][1000 genomes]
rs4860932	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860933	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860934	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860935	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62316204	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6552179	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658151	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671950	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7672364	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7696268	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs953794	0.83[ASN][1000 genomes]
rs953795	0.83[ASN][1000 genomes]
rs9990842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9991215	0.89[EUR][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	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv437385	chr4:69204755-69383357	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2319887	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69182600-69213200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:69182800-69209200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:69184200-69212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:69184200-69212800	Weak transcription	Aorta	Aorta
5	chr4:69189200-69214400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:69198600-69212800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:69199000-69213800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:69202400-69213000	Weak transcription	Fetal Stomach	stomach
9	chr4:69203000-69213400	Weak transcription	Colonic Mucosa	Colon
10	chr4:69203200-69211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:69203400-69210400	Weak transcription	Lung	lung
12	chr4:69203400-69212000	Weak transcription	HSMMtube	muscle
13	chr4:69203400-69212200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:69203400-69213000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:69203600-69210200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:69203600-69211800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:69203600-69212000	Weak transcription	Placenta	Placenta
18	chr4:69203600-69212400	Weak transcription	Fetal Kidney	kidney
19	chr4:69203600-69212600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:69203600-69213400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:69203600-69214000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:69203800-69209800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:69203800-69210000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:69203800-69213000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:69204000-69212800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr4:69204200-69209000	Enhancers	Colon Smooth Muscle	Colon
27	chr4:69204200-69212200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr4:69204400-69209200	Enhancers	Liver	Liver
29	chr4:69204400-69209600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:69204400-69212200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr4:69204400-69213600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:69204400-69213800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:69204600-69208800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:69204600-69208800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:69204600-69208800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:69204600-69210200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:69204600-69212000	Weak transcription	Fetal Thymus	thymus
38	chr4:69204600-69214600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:69204800-69212800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:69205000-69208600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:69205000-69209800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:69205000-69210000	Enhancers	Primary T cells from cord blood	blood
43	chr4:69205000-69210000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr4:69205200-69209600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:69205600-69209800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:69206800-69208400	Enhancers	Brain Hippocampus Middle	brain
47	chr4:69206800-69208800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:69206800-69208800	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr4:69207000-69208400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr4:69207000-69208600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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