Variant report

Variant	rs35898691
Chromosome Location	chr3:52130666-52130667
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	chr3:52125379..52127206-chr3:52129212..52131778,2	MCF-7	breast:
2	chr3:52090535..52092344-chr3:52130549..52132404,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10433611	1.00[AMR][1000 genomes]
rs2089225	1.00[AMR][1000 genomes]
rs323888	1.00[AMR][1000 genomes]
rs323899	1.00[AMR][1000 genomes]
rs323901	1.00[AMR][1000 genomes]
rs352646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57236484	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59196507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61333587	1.00[AMR][1000 genomes]
rs6446153	1.00[AMR][1000 genomes]
rs72955239	1.00[AMR][1000 genomes]
rs72955243	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955262	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964041	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7430706	1.00[AMR][1000 genomes]
rs7612847	1.00[AMR][1000 genomes]

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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:52115800-52133000	Weak transcription	Gastric	stomach
4	chr3:52122000-52140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52122600-52131000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:52122800-52142200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:52123600-52135200	Strong transcription	Dnd41	blood
8	chr3:52124200-52138200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:52124400-52132800	Weak transcription	Stomach Mucosa	stomach
11	chr3:52124600-52134200	Weak transcription	A549	lung
12	chr3:52124800-52142000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:52125000-52140400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:52125200-52132600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:52125400-52133400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52125400-52138400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:52125600-52132800	Strong transcription	Fetal Intestine Small	intestine
18	chr3:52125600-52135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:52125800-52132000	Weak transcription	K562	blood
20	chr3:52125800-52133400	Strong transcription	Thymus	Thymus
21	chr3:52125800-52134200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:52125800-52139800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:52125800-52142400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:52126000-52131000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52126000-52132600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:52126000-52132800	Strong transcription	Fetal Stomach	stomach
27	chr3:52126200-52135200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52126400-52132200	Weak transcription	Fetal Lung	lung
30	chr3:52126600-52132400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:52127000-52131800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:52127000-52132000	Weak transcription	Right Ventricle	heart
33	chr3:52127000-52132400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:52127000-52134600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52127200-52131800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:52127200-52132400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr3:52127400-52131600	Weak transcription	Right Atrium	heart
38	chr3:52127400-52131800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr3:52127400-52139200	Weak transcription	Esophagus	oesophagus
40	chr3:52127800-52132400	Weak transcription	Left Ventricle	heart
41	chr3:52128000-52130800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:52128200-52140800	Weak transcription	Spleen	Spleen
43	chr3:52128400-52131400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:52128400-52132000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:52128400-52132000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:52128400-52132000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:52128400-52132200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:52128400-52133000	Weak transcription	Osteobl	bone
49	chr3:52128400-52133200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:52128400-52142200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links