Variant report

Variant	rs13000260
Chromosome Location	chr2:173862542-173862543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173859019..173861377-chr2:173862387..173864335,2	MCF-7	breast:
2	chr2:173842376..173845001-chr2:173860642..173863497,2	MCF-7	breast:
3	chr2:173850441..173852065-chr2:173860790..173863463,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1011345	0.98[ASN][1000 genomes]
rs11687902	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687990	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11885983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12616563	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12624093	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12693015	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12996130	0.89[ASN][1000 genomes]
rs13413796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446981	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs1446982	0.86[EUR][1000 genomes]
rs16861125	0.98[ASN][1000 genomes]
rs16861148	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16861173	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17302307	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17374295	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823151	0.93[ASN][1000 genomes]
rs1979186	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2121483	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2166588	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2242079	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2258918	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2305461	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2592944	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2602217	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2676521	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754753	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769225	0.95[ASN][1000 genomes]
rs3769226	0.95[ASN][1000 genomes]
rs3769227	0.92[ASN][1000 genomes]
rs3769228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769229	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769231	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769236	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820840	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3820841	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3820843	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820844	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972523	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66487735	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718902	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72896070	0.97[ASN][1000 genomes]
rs72909440	0.95[ASN][1000 genomes]
rs72909444	0.95[ASN][1000 genomes]
rs72909446	0.95[ASN][1000 genomes]
rs7585997	0.81[ASN][1000 genomes]
rs7603772	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173835800-173886800	Weak transcription	Lung	lung
2	chr2:173850400-173864600	Weak transcription	Psoas Muscle	Psoas
3	chr2:173852400-173868000	Weak transcription	Gastric	stomach
4	chr2:173855800-173863400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:173856000-173885200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:173856200-173863600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:173856200-173882400	Weak transcription	Left Ventricle	heart
8	chr2:173856200-173892600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:173858400-173869000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:173858600-173862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:173859200-173863200	Weak transcription	Placenta	Placenta
12	chr2:173859800-173862600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:173860200-173863800	Enhancers	HMEC	breast
14	chr2:173860200-173864400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:173860600-173868000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:173860800-173877800	Weak transcription	Adipose Nuclei	Adipose
17	chr2:173861000-173862800	Weak transcription	Fetal Heart	heart
18	chr2:173861000-173867400	Weak transcription	Stomach Mucosa	stomach
19	chr2:173861000-173888000	Weak transcription	Fetal Stomach	stomach
20	chr2:173861200-173866800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:173861200-173867400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:173861400-173863600	Weak transcription	Fetal Lung	lung
23	chr2:173861400-173867800	Strong transcription	Liver	Liver
24	chr2:173861600-173863400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:173861600-173866800	Weak transcription	Fetal Kidney	kidney
26	chr2:173861600-173867600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:173861800-173863000	Weak transcription	Hela-S3	cervix
28	chr2:173861800-173863200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:173861800-173864800	Enhancers	A549	lung
30	chr2:173861800-173868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:173862000-173862800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:173862000-173863200	Weak transcription	NHEK	skin
33	chr2:173862000-173863400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:173862000-173864200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:173862000-173865200	Weak transcription	Ovary	ovary
36	chr2:173862200-173862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:173862200-173862600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:173862200-173867000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:173862200-173881800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:173862200-173883600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:173862400-173862800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:173862400-173870600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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