Variant report

Variant	rs17829927
Chromosome Location	chr12:105279931-105279932
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105279433..105282417-chr12:105292358..105295004,2	MCF-7	breast:
2	chr12:105277401..105280097-chr12:105289750..105292051,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10507183	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs10507185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10778356	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861278	0.86[ASN][1000 genomes]
rs10861280	0.83[ASN][1000 genomes]
rs10861282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861293	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861295	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861297	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112208	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11112221	0.90[ASN][1000 genomes]
rs11112234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230637	0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2047126	0.85[ASN][1000 genomes]
rs2245695	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249941	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252843	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2264883	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264893	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453163	0.87[ASN][1000 genomes]
rs2453164	0.87[ASN][1000 genomes]
rs2453169	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2463430	0.82[ASN][1000 genomes]
rs2468088	0.81[ASN][1000 genomes]
rs2468094	0.83[ASN][1000 genomes]
rs2468096	0.86[ASN][1000 genomes]
rs2468098	0.86[ASN][1000 genomes]
rs2468103	0.87[ASN][1000 genomes]
rs2468107	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468108	0.87[ASN][1000 genomes]
rs2468336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468338	0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468339	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468341	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468342	0.83[ASN][1000 genomes]
rs2468343	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs2468344	0.81[ASN][1000 genomes]
rs2468345	0.83[ASN][1000 genomes]
rs2468396	0.91[EUR][1000 genomes]
rs2468397	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642119	0.87[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2730294	0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs3890816	0.81[CEU][hapmap]
rs4130161	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4257060	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537841	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4630370	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4644704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964116	0.88[CEU][hapmap]
rs7959777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961766	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971260	0.87[ASN][1000 genomes]
rs7971392	0.89[ASN][1000 genomes]
rs9705471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:105260800-105280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:105267800-105284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:105273800-105288200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:105276400-105281800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105277000-105280400	Strong transcription	Liver	Liver
8	chr12:105278200-105281000	Enhancers	Fetal Lung	lung
9	chr12:105278200-105284400	Weak transcription	Aorta	Aorta
10	chr12:105278200-105284400	Weak transcription	Gastric	stomach
11	chr12:105278400-105293200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:105278600-105281600	Enhancers	Hela-S3	cervix
13	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:105279000-105280400	Weak transcription	Osteobl	bone
15	chr12:105279200-105280400	Weak transcription	NHLF	lung
16	chr12:105279600-105280000	Enhancers	A549	lung
17	chr12:105279600-105280800	Enhancers	HUVEC	blood vessel
18	chr12:105279600-105281200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:105279800-105280400	Enhancers	Stomach Mucosa	stomach

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