Variant report

Variant	rs10380
Chromosome Location	chr5:7897191-7897192
allele	C/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	CTCF	chr5:7897175-7897421	K562	blood:	n/a	n/a
2	CTCF	chr5:7897133-7897559	MCF-7	breast:	n/a	n/a
3	JUND	chr5:7897157-7897540	K562	blood:	n/a	chr5:7897362-7897369 chr5:7897359-7897370
4	MYC	chr5:7897147-7897368	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr5:7897160-7897310	NHEK	skin:	n/a	n/a
6	RAD21	chr5:7897156-7897379	K562	blood:	n/a	n/a
7	ZNF143	chr5:7897152-7897432	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr5:7897171-7897435	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr5:7897179-7897459	MCF-7	breast:	n/a	n/a
10	CTCF	chr5:7897160-7897310	HCM	heart:	n/a	n/a
11	CTCF	chr5:7897184-7897402	A549	lung:	n/a	n/a
12	FOS	chr5:7897179-7897550	MCF10A-Er-Src	breast:	n/a	chr5:7897362-7897369 chr5:7897359-7897370
13	CTCF	chr5:7897190-7897434	GM12878	blood:	n/a	n/a
14	CTCF	chr5:7897160-7897310	GM12872	blood:	n/a	n/a
15	ZNF143	chr5:7897171-7897470	GM12878	blood:	n/a	n/a
16	CTCF	chr5:7897171-7897466	K562	blood:	n/a	n/a
17	YY1	chr5:7897100-7897456	GM12878	blood:	n/a	chr5:7897338-7897350
18	CTCF	chr5:7897160-7897310	BJ	skin:	n/a	n/a
19	CTCF	chr5:7897186-7897432	LNCaP	prostate:	n/a	n/a
20	CTCF	chr5:7897160-7897310	NHDF-neo	bronchial:	n/a	n/a
21	SMC3	chr5:7897132-7897478	Hela-S3	cervix:	n/a	n/a
22	ZNF143	chr5:7897172-7897428	K562	blood:	n/a	n/a
23	CTCF	chr5:7897138-7897538	MCF-7	breast:	n/a	n/a
24	CTCF	chr5:7897184-7897452	Gliobla	brain:	n/a	n/a
25	CTCF	chr5:7897135-7897477	A549	lung:	n/a	n/a
26	RAD21	chr5:7897172-7897477	Hela-S3	cervix:	n/a	n/a
27	YY1	chr5:7897128-7897455	GM12892	blood:	n/a	chr5:7897338-7897350
28	CTCF	chr5:7897128-7897494	K562	blood:	n/a	n/a
29	FOS	chr5:7897168-7897551	MCF10A-Er-Src	breast:	n/a	chr5:7897362-7897369 chr5:7897359-7897370
30	FOSL2	chr5:7897080-7897582	A549	lung:	n/a	chr5:7897362-7897369
31	SMC3	chr5:7897155-7897437	K562	blood:	n/a	n/a
32	CTCF	chr5:7897181-7897446	T-47D	breast:	n/a	n/a
33	CTCF	chr5:7897180-7897330	HFF-Myc	foreskin:	n/a	n/a
34	FOS	chr5:7897191-7897613	HUVEC	blood vessel:	n/a	chr5:7897362-7897369 chr5:7897359-7897370
35	YY1	chr5:7897176-7897500	GM12878	blood:	n/a	chr5:7897338-7897350
36	JUND	chr5:7897138-7897518	SK-N-SH	brain:	n/a	chr5:7897362-7897369 chr5:7897359-7897370
37	CTCF	chr5:7897180-7897330	WI-38	lung:	n/a	n/a
38	FOSL2	chr5:7897095-7897557	SK-N-SH	brain:	n/a	chr5:7897362-7897369
39	RAD21	chr5:7897191-7897472	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr5:7897184-7897441	A549	lung:	n/a	n/a
41	YY1	chr5:7896917-7897735	SK-N-SH	brain:	n/a	chr5:7897338-7897350
42	RAD21	chr5:7897131-7897462	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr5:7897111-7897504	A549	lung:	n/a	chr5:7897338-7897350
44	CTCF	chr5:7897154-7897513	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr5:7897123-7897433	SK-N-SH_RA	brain:	n/a	n/a
46	YY1	chr5:7897173-7897459	SK-N-SH_RA	brain:	n/a	chr5:7897338-7897350
47	RAD21	chr5:7897189-7897417	SK-N-SH_RA	brain:	n/a	n/a
48	YY1	chr5:7897162-7897441	GM12892	blood:	n/a	chr5:7897338-7897350
49	YY1	chr5:7897161-7897590	H1-hESC	embryonic stem cell:	n/a	chr5:7897338-7897350
50	CTCF	chr5:7897124-7897511	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:7891090..7893015-chr5:7896688..7898784,2	K562	blood:
2	chr5:7896643..7897394-chr5:9498817..9499722,2	MCF-7	breast:
3	chr5:7896860..7897757-chr5:9207693..9208247,3	K562	blood:
4	chr5:7897166..7899613-chr5:7900650..7902755,2	MCF-7	breast:
5	chr5:7896681..7897358-chr5:9544262..9544852,2	K562	blood:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10063685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1046014	0.93[CEU][hapmap];0.80[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs10520874	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12347	0.81[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs162026	0.80[CHD][hapmap];0.85[MEX][hapmap]
rs162034	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs162035	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs162036	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.81[ASN][1000 genomes]
rs162039	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs162131	0.82[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs167860	0.95[ASN][1000 genomes]
rs16879305	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16879356	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16879410	0.94[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1994867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1994868	0.97[ASN][1000 genomes]
rs1994869	0.97[ASN][1000 genomes]
rs2277958	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs227872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2303079	0.89[YRI][hapmap]
rs2303081	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2613666	0.97[ASN][1000 genomes]
rs2640666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs326125	0.81[ASN][1000 genomes]
rs327574	0.97[ASN][1000 genomes]
rs327581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs327583	1.00[ASN][1000 genomes]
rs327586	0.81[ASN][1000 genomes]
rs327592	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3776454	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282639	0.85[EUR][1000 genomes]
rs4702507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap]
rs56153354	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs56219526	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57085915	0.83[AFR][1000 genomes]
rs57652931	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs57937475	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61536869	0.84[EUR][1000 genomes]
rs72716534	0.85[EUR][1000 genomes]
rs72716536	0.85[EUR][1000 genomes]
rs72716547	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7727290	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10380	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs10380	MTRR	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:7871400-7902400	Strong transcription	K562	blood
6	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:7873200-7903400	Strong transcription	Dnd41	blood
13	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
14	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
15	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
22	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:7879200-7901800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:7879200-7906400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:7879600-7900600	Strong transcription	Primary B cells from cord blood	blood
26	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:7880800-7903800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:7881000-7904400	Strong transcription	Fetal Intestine Large	intestine
31	chr5:7882200-7902200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:7882400-7898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:7882400-7905000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:7882600-7898600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:7885400-7904000	Strong transcription	A549	lung
36	chr5:7885400-7904800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:7887600-7906800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:7888000-7901400	Strong transcription	HSMM	muscle
39	chr5:7888200-7904000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:7888200-7904000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:7888200-7904200	Strong transcription	Liver	Liver
42	chr5:7888400-7903000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:7888400-7904000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr5:7888400-7904200	Strong transcription	Placenta	Placenta
45	chr5:7888400-7906400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:7888600-7897600	Strong transcription	HSMMtube	muscle
47	chr5:7888600-7900600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr5:7888600-7900600	Strong transcription	HepG2	liver
49	chr5:7888600-7900800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr5:7888600-7901800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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