Variant report

Variant	rs10888977
Chromosome Location	chr1:56997893-56997894
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	chr1:56996284..56998415-chr1:56998780..57000786,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10157636	0.81[JPT][hapmap]
rs10493211	0.84[CEU][hapmap]
rs11206833	0.95[JPT][hapmap]
rs11206838	0.84[CEU][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11583161	0.81[JPT][hapmap]
rs11590570	0.80[JPT][hapmap]
rs12081589	0.81[JPT][hapmap]
rs12082242	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134109	0.84[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1759750	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1759752	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1777274	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1777277	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1810930	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1930760	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1930762	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2017955	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4532850	0.83[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4912377	0.87[AFR][1000 genomes]
rs55798508	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6690245	0.81[JPT][hapmap]
rs7512545	0.81[JPT][hapmap]
rs7519268	0.81[JPT][hapmap]
rs7535757	0.89[MKK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7551402	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs7554557	0.81[JPT][hapmap]
rs7556056	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs953856	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs953857	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs993075	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10888977	CYB5RL	cis	parietal	SCAN
rs10888977	MRPL37	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56977800-56999200	Weak transcription	A549	lung
3	chr1:56983400-57000800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
5	chr1:56990000-57004000	Genic enhancers	Liver	Liver
6	chr1:56990200-56998600	Enhancers	Brain Substantia Nigra	brain
7	chr1:56992000-57001200	Weak transcription	Spleen	Spleen
8	chr1:56992800-56998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:56992800-56998800	Weak transcription	Gastric	stomach
10	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
11	chr1:56993000-56998800	Enhancers	Ovary	ovary
12	chr1:56993000-56999800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
14	chr1:56993200-57001400	Enhancers	Right Atrium	heart
15	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
16	chr1:56993800-56998000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:56993800-56998200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:56993800-57004200	Weak transcription	NH-A	brain
19	chr1:56994000-56998600	Weak transcription	Colonic Mucosa	Colon
20	chr1:56994000-56999000	Weak transcription	Aorta	Aorta
21	chr1:56994000-57000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:56994000-57001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
24	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
25	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
26	chr1:56994200-56998000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:56994200-56998800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:56994200-56999400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:56994200-57001200	Weak transcription	Dnd41	blood
30	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:56994400-56998400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:56994600-56998400	Enhancers	Psoas Muscle	Psoas
34	chr1:56994600-56999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:56994600-56999800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:56994800-56998000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:56994800-56999000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:56995000-56998000	Enhancers	Left Ventricle	heart
39	chr1:56995000-56998200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:56995000-56998200	Strong transcription	Fetal Stomach	stomach
41	chr1:56995000-56998400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:56995000-57003600	Strong transcription	Osteobl	bone
44	chr1:56995200-56999800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:56995200-57000000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:56995400-56998000	Weak transcription	Small Intestine	intestine
48	chr1:56995600-57000000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:56995800-56998800	Enhancers	Fetal Heart	heart

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