Variant report

Variant	rs11681098
Chromosome Location	chr2:20341401-20341402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20339624..20342165-chr2:20377427..20379627,2	MCF-7	breast:
2	chr2:20339085..20342472-chr2:20423040..20426364,5	MCF-7	breast:
3	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
4	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
5	chr2:20313769..20315604-chr2:20340680..20342893,2	MCF-7	breast:
6	chr2:20335603..20338539-chr2:20339889..20342133,4	K562	blood:
7	chr2:20332851..20335555-chr2:20339124..20341592,3	K562	blood:
8	chr2:20335576..20338444-chr2:20340414..20343314,2	MCF-7	breast:
9	chr2:20337465..20342202-chr2:20382545..20388364,6	MCF-7	breast:
10	chr2:20338664..20345614-chr2:20377409..20381353,9	MCF-7	breast:
11	chr2:20341298..20344262-chr2:20354699..20358501,3	MCF-7	breast:
12	chr2:20339841..20342282-chr2:20379713..20382419,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213729	Chromatin interaction
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11686716	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1398949	1.00[JPT][hapmap]
rs1398950	0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17652287	0.90[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55719360	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs907863	0.84[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11681098	SDC1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20334200-20346600	Enhancers	Placenta	Placenta
3	chr2:20335800-20343400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:20336800-20341800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:20337400-20343400	Enhancers	NHEK	skin
7	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:20338000-20346800	Enhancers	HMEC	breast
9	chr2:20338200-20342200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:20338400-20342000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:20339400-20341600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:20339600-20341800	Bivalent Enhancer	HepG2	liver
13	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
14	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:20340000-20345200	Weak transcription	Fetal Lung	lung
16	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:20340200-20342800	Weak transcription	Fetal Intestine Small	intestine
19	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:20340400-20342000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:20340400-20342000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:20340400-20342400	Weak transcription	Fetal Intestine Large	intestine
23	chr2:20340600-20341600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:20340600-20341800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:20340600-20341800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:20340600-20341800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:20340600-20341800	Enhancers	Liver	Liver
28	chr2:20340600-20342000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:20340600-20342000	Enhancers	HUVEC	blood vessel
30	chr2:20340600-20342000	Enhancers	NHDF-Ad	bronchial
31	chr2:20340600-20342000	Enhancers	NHLF	lung
32	chr2:20340600-20342200	Enhancers	NH-A	brain
33	chr2:20340600-20343200	Enhancers	Esophagus	oesophagus
34	chr2:20340600-20343400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:20340800-20341600	Flanking Active TSS	Hela-S3	cervix
36	chr2:20340800-20341600	Enhancers	HSMM	muscle
37	chr2:20340800-20341800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr2:20340800-20342000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:20340800-20342000	Enhancers	Osteobl	bone
40	chr2:20340800-20342400	Enhancers	Stomach Mucosa	stomach
41	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:20341000-20341600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:20341000-20341600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:20341000-20341800	Enhancers	Adipose Nuclei	Adipose
45	chr2:20341000-20342000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr2:20341000-20342000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:20341000-20344800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:20341200-20341600	Enhancers	K562	blood
49	chr2:20341200-20341800	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:20341200-20344800	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links