Variant report

Variant	rs59846661
Chromosome Location	chr1:173986013-173986014
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173982774..173988202-chr1:173988612..173994506,10	MCF-7	breast:
2	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1322769	1.00[AMR][1000 genomes]
rs16846483	1.00[AMR][1000 genomes]
rs2227620	1.00[AMR][1000 genomes]
rs57006357	1.00[AMR][1000 genomes]
rs57343517	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57664780	1.00[AMR][1000 genomes]
rs58576036	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58735809	1.00[AMR][1000 genomes]
rs58930477	1.00[AMR][1000 genomes]
rs59355797	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60229445	0.85[AFR][1000 genomes]
rs6667627	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6704413	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025612	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025620	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025635	0.81[AFR][1000 genomes]
rs73027407	1.00[AMR][1000 genomes]
rs73027443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027460	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027463	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027464	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027488	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036625	1.00[AMR][1000 genomes]
rs73036632	1.00[AMR][1000 genomes]
rs73036635	1.00[AMR][1000 genomes]
rs73037076	1.00[AMR][1000 genomes]
rs73037083	1.00[AMR][1000 genomes]
rs73037097	1.00[AMR][1000 genomes]
rs73041050	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73041059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7519571	1.00[AMR][1000 genomes]
rs7531236	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547873	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9726181	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
2	chr1:173958600-173987200	Weak transcription	Gastric	stomach
3	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:173962200-173989000	Weak transcription	Fetal Kidney	kidney
5	chr1:173962200-173989600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:173962200-173989600	Weak transcription	Aorta	Aorta
7	chr1:173962200-173989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:173962200-173990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:173962400-173987800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:173962600-173988400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:173962600-173988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:173962600-173989400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:173962800-173989800	Weak transcription	Placenta	Placenta
14	chr1:173965000-173989600	Weak transcription	Fetal Thymus	thymus
15	chr1:173965200-173986600	Weak transcription	HUVEC	blood vessel
16	chr1:173966200-173986200	Weak transcription	Fetal Brain Female	brain
17	chr1:173966200-173989800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:173966400-173986600	Weak transcription	Thymus	Thymus
19	chr1:173966400-173987800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:173966400-173989600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:173966400-173989800	Weak transcription	Esophagus	oesophagus
22	chr1:173967800-173987600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:173968400-173987200	Weak transcription	Fetal Intestine Large	intestine
24	chr1:173971200-173988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:173974600-173986400	Weak transcription	HSMM	muscle
26	chr1:173975000-173986400	Weak transcription	HMEC	breast
27	chr1:173975200-173987200	Weak transcription	NHLF	lung
28	chr1:173975400-173987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:173975600-173986200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:173975800-173986400	Weak transcription	NHDF-Ad	bronchial
31	chr1:173976600-173990000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:173976800-173986400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:173977000-173986400	Weak transcription	Fetal Stomach	stomach
34	chr1:173977200-173986400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:173977200-173989200	Weak transcription	NH-A	brain
36	chr1:173977800-173987200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:173977800-173988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:173978600-173986600	Weak transcription	Hela-S3	cervix
39	chr1:173978600-173989200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:173978800-173986600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:173978800-173990200	Weak transcription	Spleen	Spleen
42	chr1:173979000-173987000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:173979000-173987000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:173979000-173987800	Weak transcription	Right Atrium	heart
45	chr1:173979400-173987000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:173979400-173989200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:173979800-173989600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:173980000-173986600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:173981000-173986400	Weak transcription	Fetal Lung	lung
50	chr1:173981200-173987600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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