Variant report

Variant	rs61018457
Chromosome Location	chr1:220281821-220281822
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	chr1:220279596..220282587-chr1:220284758..220287286,2	MCF-7	breast:
2	chr1:220279805..220282778-chr1:220291270..220293598,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB3GAP2-1	chr1:220281670-220281887	NONHSAT009579

Variant related genes	Relation type
ENSG00000207590	Chromatin interaction
ENSG00000207624	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11805285	0.84[EUR][1000 genomes]
rs17007135	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577152	0.87[ASN][1000 genomes]
rs3754060	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59914129	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59991104	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60736051	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61569366	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73096557	0.88[ASN][1000 genomes]
rs73096599	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098515	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73098558	0.84[EUR][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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:220268400-220287400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
4	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:220268600-220282600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:220269200-220282400	Weak transcription	Spleen	Spleen
8	chr1:220269200-220282600	Weak transcription	Esophagus	oesophagus
9	chr1:220269200-220285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:220269200-220291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:220269200-220291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:220269200-220292800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:220269400-220283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:220269400-220284800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:220269400-220284800	Strong transcription	Osteobl	bone
17	chr1:220269400-220291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:220269600-220290600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:220269600-220291200	Strong transcription	Liver	Liver
21	chr1:220269600-220291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:220269600-220291400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:220269600-220291400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:220269600-220291600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:220269600-220291800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:220269800-220284800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:220269800-220284800	Strong transcription	Fetal Intestine Large	intestine
28	chr1:220269800-220286400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:220269800-220286600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:220269800-220291000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:220269800-220291200	Strong transcription	Fetal Thymus	thymus
32	chr1:220269800-220291600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:220269800-220292800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:220270000-220291200	Strong transcription	Placenta	Placenta
35	chr1:220270000-220291600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:220270000-220292800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:220270400-220290000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:220270400-220291600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:220270600-220285000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:220270600-220293800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:220271000-220285600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:220271000-220286200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:220271000-220286200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:220271000-220292000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:220272000-220293200	Strong transcription	Dnd41	blood
46	chr1:220272200-220284800	Strong transcription	Brain Anterior Caudate	brain
47	chr1:220272800-220283400	Strong transcription	Primary B cells from cord blood	blood
48	chr1:220273400-220287400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:220273800-220285400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:220274000-220284600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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