Variant report

Variant	rs12494777
Chromosome Location	chr3:113374646-113374647
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	chr3:113371111..113372723-chr3:113373637..113375843,2	MCF-7	breast:
2	chr3:113373464..113375061-chr3:113414859..113416846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176542	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10934239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10934240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11914863	1.00[ASN][1000 genomes]
rs11918910	1.00[ASN][1000 genomes]
rs11920913	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11921407	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12486414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12490048	0.93[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12492290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12492783	0.93[AMR][1000 genomes]
rs12493602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12493935	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12495298	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12495713	1.00[AMR][1000 genomes]
rs12496604	1.00[AMR][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12497754	1.00[AMR][1000 genomes]
rs16861230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861235	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861331	1.00[AMR][1000 genomes]
rs2292512	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2566972	0.87[AMR][1000 genomes]
rs2603791	0.87[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58929900	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113342600-113375800	Weak transcription	Pancreas	Pancrea
2	chr3:113365800-113375200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:113366000-113376200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:113366000-113377000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113366000-113377000	Weak transcription	Liver	Liver
6	chr3:113366200-113375400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:113366400-113375800	Weak transcription	Spleen	Spleen
8	chr3:113366600-113374800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:113366800-113378800	Weak transcription	Gastric	stomach
10	chr3:113367200-113377600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:113368000-113376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:113368000-113376200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:113368000-113383400	Weak transcription	Colonic Mucosa	Colon
14	chr3:113368400-113377200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:113368600-113375800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:113368800-113376800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:113369000-113377200	Weak transcription	Ovary	ovary
18	chr3:113370000-113374800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:113370400-113378000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:113371200-113377200	Weak transcription	Fetal Brain Male	brain
21	chr3:113371200-113379400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:113371600-113382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:113371800-113386800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:113372000-113374800	Weak transcription	Adipose Nuclei	Adipose
25	chr3:113372200-113374800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:113372200-113376000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:113372400-113378200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:113372400-113378600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:113372600-113375800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:113372600-113376400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:113372600-113376600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:113372600-113377600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:113373000-113375000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:113373000-113375600	Weak transcription	Placenta	Placenta
35	chr3:113373000-113375800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:113373000-113375800	Weak transcription	HepG2	liver
37	chr3:113373000-113377400	Weak transcription	NHLF	lung
38	chr3:113373000-113377600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:113373000-113377600	Weak transcription	Esophagus	oesophagus
40	chr3:113373200-113375000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:113373200-113377000	Weak transcription	Dnd41	blood
42	chr3:113373200-113377800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:113373200-113378200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:113373200-113383800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:113373200-113386800	Weak transcription	HUVEC	blood vessel
46	chr3:113373400-113375000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:113373400-113378000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:113373400-113384600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:113373600-113378600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:113373600-113379200	Strong transcription	Muscle Satellite Cultured Cells	--

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