Variant report

Variant	rs1261411
Chromosome Location	chr1:57017739-57017740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57015989..57018935-chr1:57031658..57034048,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10888979	0.83[JPT][hapmap]
rs11206839	0.83[JPT][hapmap]
rs11206840	0.80[JPT][hapmap]
rs11206841	0.83[JPT][hapmap]
rs11576602	0.80[TSI][hapmap]
rs1930760	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1930762	0.82[ASW][hapmap]
rs4912377	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7529520	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs7535757	0.88[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7556056	0.82[ASW][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1261411	RPE	trans	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57001200-57018800	Weak transcription	A549	lung
2	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
3	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:57002800-57018600	Weak transcription	Thymus	Thymus
5	chr1:57003200-57019800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:57007400-57028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:57009600-57028000	Weak transcription	Fetal Kidney	kidney
8	chr1:57010400-57019200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:57010400-57019600	Enhancers	Right Ventricle	heart
10	chr1:57011000-57020200	Enhancers	Brain Hippocampus Middle	brain
11	chr1:57011800-57018000	Enhancers	Brain Substantia Nigra	brain
12	chr1:57012200-57017800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr1:57012600-57019200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:57012600-57019600	Enhancers	Brain Angular Gyrus	brain
15	chr1:57012600-57020000	Enhancers	Adipose Nuclei	Adipose
16	chr1:57013000-57017800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:57013000-57019400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:57013000-57019400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr1:57013000-57019400	Enhancers	Psoas Muscle	Psoas
20	chr1:57013000-57019800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:57013000-57020000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:57013200-57017800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:57013200-57017800	Enhancers	Right Atrium	heart
24	chr1:57013200-57018000	Enhancers	Ovary	ovary
25	chr1:57013200-57019200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:57013200-57021000	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:57013400-57017800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:57013400-57018600	Enhancers	Liver	Liver
29	chr1:57014000-57026000	Weak transcription	Fetal Intestine Large	intestine
30	chr1:57014400-57018800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:57014800-57017800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:57014800-57019000	Weak transcription	Osteobl	bone
33	chr1:57014800-57019600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:57015000-57017800	Enhancers	Colon Smooth Muscle	Colon
35	chr1:57015000-57019000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:57015200-57018600	Strong transcription	NHLF	lung
37	chr1:57015200-57019000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:57015200-57019400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:57015400-57017800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:57015400-57018000	Enhancers	Left Ventricle	heart
41	chr1:57015600-57017800	Enhancers	Pancreas	Pancrea
42	chr1:57015600-57018600	Enhancers	Fetal Brain Male	brain
43	chr1:57015800-57019800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr1:57015800-57021200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
46	chr1:57016200-57017800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:57016200-57017800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:57016200-57018000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:57016200-57020000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:57016400-57017800	Enhancers	Fetal Heart	heart

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