Variant report

Variant	rs72979701
Chromosome Location	chr3:135693597-135693598
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135683614..135686835-chr3:135692106..135694532,3	MCF-7	breast:
2	chr3:135693339..135695483-chr3:135697510..135700287,2	MCF-7	breast:
3	chr3:135634384..135636473-chr3:135692724..135694710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11918906	1.00[EUR][1000 genomes]
rs11925256	1.00[EUR][1000 genomes]
rs1403765	1.00[AFR][1000 genomes]
rs16843517	1.00[AFR][1000 genomes]
rs16843565	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16843571	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16843592	1.00[EUR][1000 genomes]
rs16843601	1.00[AFR][1000 genomes]
rs16843602	1.00[AFR][1000 genomes]
rs16843633	1.00[EUR][1000 genomes]
rs16843656	1.00[AFR][1000 genomes]
rs16843661	1.00[EUR][1000 genomes]
rs56848754	0.91[AFR][1000 genomes]
rs57374999	1.00[EUR][1000 genomes]
rs57507646	1.00[AFR][1000 genomes]
rs57524286	1.00[AFR][1000 genomes]
rs57539640	1.00[AFR][1000 genomes]
rs57578189	1.00[AFR][1000 genomes]
rs57681844	1.00[AFR][1000 genomes]
rs58030391	1.00[EUR][1000 genomes]
rs58136416	0.83[AFR][1000 genomes]
rs58362057	1.00[AFR][1000 genomes]
rs58619345	1.00[AFR][1000 genomes]
rs59899876	1.00[AFR][1000 genomes]
rs59985031	1.00[AFR][1000 genomes]
rs60165730	1.00[EUR][1000 genomes]
rs60393211	1.00[EUR][1000 genomes]
rs61209689	1.00[EUR][1000 genomes]
rs61216931	1.00[AFR][1000 genomes]
rs72977692	0.81[AFR][1000 genomes]
rs72977699	0.81[AFR][1000 genomes]
rs72977700	0.81[AFR][1000 genomes]
rs72979626	0.91[AFR][1000 genomes]
rs72979633	0.91[AFR][1000 genomes]
rs72979636	0.91[AFR][1000 genomes]
rs72979647	1.00[AFR][1000 genomes]
rs72979686	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979693	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979696	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72981430	0.83[AFR][1000 genomes]
rs72981436	1.00[AFR][1000 genomes]
rs72981447	1.00[AFR][1000 genomes]
rs72981448	1.00[AFR][1000 genomes]
rs72981456	1.00[AFR][1000 genomes]
rs72981481	1.00[EUR][1000 genomes]
rs72981494	1.00[EUR][1000 genomes]
rs72981499	1.00[AFR][1000 genomes]
rs72983403	1.00[EUR][1000 genomes]
rs72983409	1.00[EUR][1000 genomes]
rs72983435	1.00[AFR][1000 genomes]
rs72983437	1.00[EUR][1000 genomes]
rs72983449	1.00[EUR][1000 genomes]
rs72983458	1.00[AFR][1000 genomes]
rs72983460	1.00[EUR][1000 genomes]
rs72983467	0.83[AFR][1000 genomes]
rs72983501	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135685600-135693800	Weak transcription	Gastric	stomach
2	chr3:135685800-135693800	Weak transcription	Lung	lung
3	chr3:135686600-135694400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:135687600-135694000	Enhancers	Colon Smooth Muscle	Colon
5	chr3:135687600-135700400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:135688000-135694200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:135688800-135694200	Enhancers	Brain Substantia Nigra	brain
8	chr3:135689400-135695200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:135690200-135694200	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:135690200-135701200	Weak transcription	NHEK	skin
11	chr3:135690200-135701400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:135690400-135694000	Weak transcription	HMEC	breast
13	chr3:135690400-135700800	Weak transcription	HSMM	muscle
14	chr3:135690800-135693800	Weak transcription	NHDF-Ad	bronchial
15	chr3:135691000-135699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:135691200-135699600	Weak transcription	Ovary	ovary
17	chr3:135691600-135694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:135691600-135694200	Enhancers	Brain Angular Gyrus	brain
19	chr3:135691600-135694400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:135691800-135693600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:135691800-135693800	Enhancers	Stomach Mucosa	stomach
22	chr3:135692200-135694000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:135692200-135694200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:135692200-135694200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:135692200-135694200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:135692200-135694200	Enhancers	Psoas Muscle	Psoas
27	chr3:135692400-135694000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:135692400-135694400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:135692600-135693600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:135692600-135693800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:135692600-135693800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:135692600-135694000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:135692600-135694000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:135692600-135694000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:135692600-135694200	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:135692600-135694200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:135692600-135694200	Enhancers	Fetal Heart	heart
38	chr3:135692800-135693600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:135692800-135693600	Enhancers	Brain Anterior Caudate	brain
40	chr3:135692800-135693600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:135692800-135693600	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:135692800-135694000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:135692800-135694000	Enhancers	Aorta	Aorta
44	chr3:135692800-135694000	Enhancers	Esophagus	oesophagus
45	chr3:135692800-135694200	Enhancers	Right Atrium	heart
46	chr3:135692800-135694200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:135693000-135693600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:135693000-135693600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:135693000-135700600	Weak transcription	Pancreas	Pancrea
50	chr3:135693000-135701400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links