Variant report

Variant	rs12490054
Chromosome Location	chr3:99667823-99667824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99665125..99667947-chr3:99677482..99680159,2	MCF-7	breast:
2	chr3:99666008..99667962-chr3:99668003..99670622,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12493320	1.00[CHB][hapmap]
rs34518627	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635633	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99663400-99669800	Weak transcription	NHLF	lung
3	chr3:99663400-99671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:99663600-99669400	Weak transcription	NH-A	brain
5	chr3:99664400-99669400	Weak transcription	Pancreas	Pancrea
6	chr3:99664400-99672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:99664400-99672600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:99664400-99672600	Weak transcription	Gastric	stomach
9	chr3:99664400-99674800	Weak transcription	Right Atrium	heart
10	chr3:99664600-99668200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:99664600-99669400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:99664600-99669800	Weak transcription	HSMMtube	muscle
13	chr3:99664600-99672200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:99664600-99676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:99664800-99668200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:99664800-99668200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:99664800-99668400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:99664800-99669600	Weak transcription	HSMM	muscle
19	chr3:99664800-99669800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:99664800-99669800	Weak transcription	Osteobl	bone
21	chr3:99664800-99670400	Weak transcription	NHDF-Ad	bronchial
22	chr3:99664800-99670800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:99664800-99672600	Weak transcription	Left Ventricle	heart
24	chr3:99664800-99672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:99664800-99677200	Weak transcription	Esophagus	oesophagus
26	chr3:99664800-99677200	Weak transcription	Ovary	ovary
27	chr3:99665000-99669800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:99665000-99670000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:99665000-99670000	Weak transcription	Small Intestine	intestine
30	chr3:99665000-99672400	Weak transcription	Fetal Heart	heart
31	chr3:99665000-99677200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:99665000-99677200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:99665000-99678800	Weak transcription	Aorta	Aorta
34	chr3:99665200-99673800	Weak transcription	Fetal Lung	lung
35	chr3:99665400-99668400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:99665600-99669800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:99665600-99671000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:99665800-99669800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:99666400-99669200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:99666400-99669800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:99666400-99672200	Weak transcription	Psoas Muscle	Psoas
42	chr3:99666600-99669800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:99667000-99669000	Enhancers	K562	blood
44	chr3:99667200-99668000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:99667400-99668000	Enhancers	Colon Smooth Muscle	Colon
46	chr3:99667400-99669000	Enhancers	A549	lung
47	chr3:99667600-99668600	Enhancers	Fetal Intestine Small	intestine
48	chr3:99667600-99670200	Enhancers	Stomach Mucosa	stomach
49	chr3:99667800-99668200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:99667800-99668200	Weak transcription	Placenta Amnion	Placenta Amnion

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