Variant report

Variant	rs17041625
Chromosome Location	chr2:111706085-111706086
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	chr2:111706009..111708285-chr2:111713250..111715688,2	MCF-7	breast:
2	chr2:111695965..111698914-chr2:111704650..111707242,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13003854	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1554004	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17524344	1.00[CHD][hapmap]
rs2341917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35300924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7596265	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1004949	chr2:111607532-111780719	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1002568	chr2:111607532-111781442	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1005665	chr2:111610107-111762039	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535892	chr2:111610107-111762039	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17041625	SULT1C2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111693000-111706400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111704000-111706400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:111704200-111706600	Enhancers	Fetal Heart	heart
4	chr2:111704200-111706800	Enhancers	Fetal Muscle Trunk	muscle
5	chr2:111704200-111706800	Enhancers	Left Ventricle	heart
6	chr2:111704200-111707000	Enhancers	Fetal Muscle Leg	muscle
7	chr2:111704200-111709600	Enhancers	Fetal Lung	lung
8	chr2:111704400-111706200	Enhancers	Adipose Nuclei	Adipose
9	chr2:111704600-111706600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:111704600-111707000	Enhancers	Right Atrium	heart
11	chr2:111704800-111706200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:111704800-111707200	Enhancers	Fetal Stomach	stomach
13	chr2:111705200-111706200	Enhancers	Fetal Intestine Small	intestine
14	chr2:111705200-111706400	Enhancers	Colon Smooth Muscle	Colon
15	chr2:111705400-111706600	Enhancers	Fetal Intestine Large	intestine
16	chr2:111705400-111706800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:111705600-111706200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:111705600-111706200	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:111705600-111706200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:111705600-111706200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:111705600-111706600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:111705600-111706600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:111705800-111706200	Weak transcription	Lung	lung
24	chr2:111705800-111706200	Weak transcription	Right Ventricle	heart
25	chr2:111705800-111706600	Enhancers	Brain Germinal Matrix	brain
26	chr2:111706000-111706200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links