Variant report

Variant	rs73830614
Chromosome Location	chr3:45959026-45959027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:45958909-45959235	K562	blood:	n/a	n/a
2	POLR2A	chr3:45958948-45959142	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:45958608-45959091	GM12891	blood:	n/a	n/a
4	STAT3	chr3:45958934-45959370	MCF10A-Er-Src	breast:	n/a	chr3:45959250-45959258
5	POLR2A	chr3:45957672-45959751	K562	blood:	n/a	n/a
6	POLR2A	chr3:45958641-45959126	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:45958646-45959141	HL-60	blood:	n/a	n/a
8	MYC	chr3:45958972-45959497	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:45958675-45959049	K562	blood:	n/a	n/a
10	STAT3	chr3:45958958-45959324	MCF10A-Er-Src	breast:	n/a	chr3:45959250-45959258

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45957988..45959492-chr3:45959750..45961379,2	K562	blood:
2	chr3:45958439..45960531-chr3:46002605..46005170,2	K562	blood:

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2234352	0.81[AFR][1000 genomes]
rs55668304	1.00[AFR][1000 genomes]
rs59842697	0.96[AFR][1000 genomes]
rs60091281	0.96[AFR][1000 genomes]
rs73830632	0.84[AFR][1000 genomes]
rs73830666	0.81[AFR][1000 genomes]
rs73830667	0.84[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
3	chr3:45940000-45959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:45941400-45960000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:45943600-45961200	Weak transcription	Gastric	stomach
7	chr3:45946200-45960400	Weak transcription	Aorta	Aorta
8	chr3:45947000-45960200	Weak transcription	Lung	lung
9	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:45948800-45960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:45949800-45962600	Weak transcription	HepG2	liver
14	chr3:45950000-45960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:45950200-45959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:45950200-45960000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:45950200-45960400	Weak transcription	Pancreas	Pancrea
18	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
19	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
20	chr3:45953200-45959200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:45953200-45959600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:45953200-45960800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:45953400-45959800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:45955800-45960000	Weak transcription	Fetal Intestine Large	intestine
25	chr3:45956200-45959400	Flanking Active TSS	Thymus	Thymus
26	chr3:45956400-45959600	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:45956600-45960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:45956800-45961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:45957000-45959400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:45957000-45959400	Enhancers	HMEC	breast
31	chr3:45957200-45959400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:45957400-45960800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:45957400-45961600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:45957600-45959200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:45957600-45959400	Enhancers	Esophagus	oesophagus
37	chr3:45957600-45960000	Weak transcription	Fetal Lung	lung
38	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:45957800-45960000	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:45957800-45960200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:45957800-45960200	Weak transcription	Left Ventricle	heart
42	chr3:45957800-45960800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:45957800-45961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:45957800-45961400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links