Variant report

Variant	rs6688710
Chromosome Location	chr1:45218542-45218543
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	chr1:45185461..45187153-chr1:45217783..45220388,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10127448	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465818	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211030	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211031	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211034	0.90[ASN][1000 genomes]
rs11584031	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11801067	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808189	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808852	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059964	0.81[CEU][hapmap]
rs12094028	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117881	0.83[ASN][1000 genomes]
rs12136048	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136099	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410588	0.84[ASN][1000 genomes]
rs12742914	0.90[ASN][1000 genomes]
rs16832228	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263986	0.81[JPT][hapmap]
rs4542248	0.82[EUR][1000 genomes]
rs6429548	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6656337	0.92[ASN][1000 genomes]
rs6658470	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666987	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671255	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678729	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685176	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7512710	0.98[ASN][1000 genomes]
rs7518836	0.93[ASN][1000 genomes]
rs7524446	0.87[CEU][hapmap]
rs7525308	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7536146	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550170	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9988580	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats 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	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6688710	EIF2B3	cis	cerebellum	SCAN
rs6688710	EIF2B3	cis	parietal	SCAN
rs6688710	UROD	cis	multi-tissue	Pritchard
rs6688710	SNORD38B	cis	cerebellum	SCAN
rs6688710	C1orf84	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45223400	Weak transcription	Lung	lung
3	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
4	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:45206200-45220000	Weak transcription	Spleen	Spleen
6	chr1:45206200-45224800	Weak transcription	Esophagus	oesophagus
7	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
9	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
12	chr1:45206400-45218600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:45206400-45219000	Weak transcription	Primary B cells from cord blood	blood
14	chr1:45206400-45219600	Weak transcription	Placenta	Placenta
15	chr1:45206400-45221400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:45206800-45223000	Weak transcription	Fetal Kidney	kidney
20	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
21	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:45207000-45218800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:45209200-45218600	Weak transcription	Brain Germinal Matrix	brain
33	chr1:45209200-45221600	Weak transcription	Fetal Heart	heart
34	chr1:45209400-45235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:45211200-45233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:45211400-45218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:45211400-45229400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:45211400-45233600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:45211400-45234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:45211400-45235000	Strong transcription	Fetal Stomach	stomach
41	chr1:45211600-45231200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:45211600-45234600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:45211600-45235200	Strong transcription	Thymus	Thymus
44	chr1:45211800-45229400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:45211800-45229400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:45212000-45224600	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:45212000-45235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:45212000-45235200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:45212400-45220000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:45212400-45234800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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