Variant report

Variant	rs6552179
Chromosome Location	chr4:69204755-69204756
allele	C/G
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	chr4:69204549-69204949	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:69200762..69202347-chr4:69204552..69206284,2	MCF-7	breast:
2	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: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10003465	0.86[EUR][1000 genomes]
rs10471153	0.83[ASN][1000 genomes]
rs11131746	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11735530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12331971	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13121372	0.83[ASN][1000 genomes]
rs13127027	0.83[ASN][1000 genomes]
rs13145544	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1320797	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406695	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1406696	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17089240	0.95[CEU][hapmap];0.83[ASN][1000 genomes]
rs17089241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1715086	0.83[ASN][1000 genomes]
rs1730872	0.95[ASN][1000 genomes]
rs1730875	0.83[ASN][1000 genomes]
rs1880183	0.95[ASN][1000 genomes]
rs1919905	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962172	0.83[ASN][1000 genomes]
rs2140519	0.95[ASN][1000 genomes]
rs2319887	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34032921	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34186169	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34223548	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34282559	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34527218	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34896019	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35051311	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797007	0.82[ASN][1000 genomes]
rs3927373	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860292	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860927	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860928	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4860930	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860932	0.87[ASN][1000 genomes]
rs4860933	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860934	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860935	0.87[ASN][1000 genomes]
rs6822778	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658151	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678448	0.88[EUR][1000 genomes]
rs953794	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs953795	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9990842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[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	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
rs6552179	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69178000-69205000	Strong transcription	Dnd41	blood
2	chr4:69182600-69213200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:69182800-69207200	Weak transcription	Small Intestine	intestine
4	chr4:69182800-69209200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:69183000-69207800	Weak transcription	Esophagus	oesophagus
6	chr4:69184200-69207800	Weak transcription	Spleen	Spleen
7	chr4:69184200-69212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:69184200-69212800	Weak transcription	Aorta	Aorta
9	chr4:69185400-69204800	Weak transcription	Stomach Mucosa	stomach
10	chr4:69189200-69214400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:69194800-69207800	Weak transcription	Hela-S3	cervix
12	chr4:69195800-69207800	Weak transcription	Psoas Muscle	Psoas
13	chr4:69198600-69212800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:69199000-69213800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:69200400-69206600	Weak transcription	Primary B cells from cord blood	blood
16	chr4:69200600-69204800	Weak transcription	Fetal Intestine Small	intestine
17	chr4:69202400-69213000	Weak transcription	Fetal Stomach	stomach
18	chr4:69202600-69204800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:69203000-69213400	Weak transcription	Colonic Mucosa	Colon
20	chr4:69203200-69205000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:69203200-69207400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:69203200-69207600	Weak transcription	K562	blood
23	chr4:69203200-69207800	Weak transcription	Ovary	ovary
24	chr4:69203200-69208000	Weak transcription	NHLF	lung
25	chr4:69203200-69211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:69203400-69204800	Weak transcription	Brain Anterior Caudate	brain
27	chr4:69203400-69204800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:69203400-69205200	Weak transcription	Fetal Lung	lung
29	chr4:69203400-69205200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:69203400-69205800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:69203400-69205800	Weak transcription	HUVEC	blood vessel
32	chr4:69203400-69206000	Enhancers	Brain Angular Gyrus	brain
33	chr4:69203400-69207200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:69203400-69207600	Weak transcription	Fetal Brain Male	brain
35	chr4:69203400-69210400	Weak transcription	Lung	lung
36	chr4:69203400-69212000	Weak transcription	HSMMtube	muscle
37	chr4:69203400-69212200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:69203400-69213000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:69203600-69204800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:69203600-69205000	Weak transcription	Primary T cells from cord blood	blood
41	chr4:69203600-69205000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:69203600-69205400	Weak transcription	Fetal Intestine Large	intestine
43	chr4:69203600-69206000	Weak transcription	A549	lung
44	chr4:69203600-69206800	Weak transcription	HSMM	muscle
45	chr4:69203600-69207000	Weak transcription	GM12878-XiMat	blood
46	chr4:69203600-69207200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:69203600-69207200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:69203600-69207200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:69203600-69207200	Weak transcription	HepG2	liver
50	chr4:69203600-69207600	Weak transcription	NH-A	brain

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