Variant report

Variant	rs10178028
Chromosome Location	chr2:148961045-148961046
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	chr2:148960078..148961760-chr2:148963590..148966098,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13389636	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396922	0.86[ASN][1000 genomes]
rs13397840	0.86[ASN][1000 genomes]
rs16828420	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840139	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982387	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477138	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34521647	0.84[ASN][1000 genomes]
rs6731657	0.82[CHB][hapmap]
rs67576946	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv915953	chr2:148934787-148977722	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148913000-148977600	Weak transcription	Aorta	Aorta
2	chr2:148928600-148993600	Weak transcription	HSMM	muscle
3	chr2:148931200-148993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:148938400-148969200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:148943800-148961200	Weak transcription	Fetal Lung	lung
6	chr2:148944000-148987400	Weak transcription	Ovary	ovary
7	chr2:148944200-148978400	Weak transcription	Left Ventricle	heart
8	chr2:148944400-148962200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:148944600-148978400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:148958800-148964200	Weak transcription	Adipose Nuclei	Adipose
11	chr2:148959000-148967600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:148959200-148987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:148959400-148966800	Weak transcription	Pancreas	Pancrea
14	chr2:148959400-148978400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:148959400-148987000	Weak transcription	Primary B cells from cord blood	blood
16	chr2:148959400-148993400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:148959600-148964600	Weak transcription	Fetal Intestine Small	intestine
18	chr2:148959600-148970000	Weak transcription	Thymus	Thymus
19	chr2:148959600-148972400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:148959600-148978600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:148959600-148986800	Weak transcription	Primary T cells from cord blood	blood
22	chr2:148959800-148962800	Weak transcription	Fetal Brain Male	brain
23	chr2:148960000-148967200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:148960000-148967400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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