Variant report

Variant	rs358744
Chromosome Location	chr3:155463262-155463263
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	SP1	chr3:155461843-155463352	A549	lung:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
2	EBF1	chr3:155462961-155463332	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:155462962-155463280	K562	blood:	n/a	n/a
4	MAZ	chr3:155462279-155463294	IMR90	lung:	n/a	chr3:155462885-155462895
5	MAX	chr3:155462581-155463283	A549	lung:	n/a	chr3:155462885-155462895
6	E2F6	chr3:155462743-155463298	H1-hESC	embryonic stem cell:	n/a	chr3:155462857-155462866
7	MXI1	chr3:155461328-155463302	SK-N-SH	brain:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
8	SP1	chr3:155461785-155463302	HCT-116	colon:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
9	SP1	chr3:155462509-155463360	A549	lung:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
10	TCF12	chr3:155461824-155464128	A549	lung:	n/a	n/a
11	MAX	chr3:155461626-155463325	A549	lung:	n/a	chr3:155461990-155461999 chr3:155462885-155462895

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155463918-chr3:155586998..155589713,4	K562	blood:
2	chr3:155462983..155464516-chr3:156391624..156393774,2	MCF-7	breast:
3	chr3:155461195..155464539-chr3:155588373..155590107,3	MCF-7	breast:
4	chr3:155460891..155464537-chr3:155570941..155574143,3	MCF-7	breast:
5	chr3:155462054..155464221-chr3:155571081..155573574,2	MCF-7	breast:
6	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
7	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:

Variant related genes	Relation type
PLCH1	TF binding region
ENSG00000214919	TF binding region
ENSG00000163655	Chromatin interaction
ENSG00000169359	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10936015	0.80[EUR][1000 genomes]
rs11923772	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs173370	0.80[EUR][1000 genomes]
rs181588	0.80[EUR][1000 genomes]
rs184836	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2320190	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs358714	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs358720	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs358722	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358736	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358738	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358740	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358741	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358745	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358746	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358748	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs396797	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs400999	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680215	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57183957	0.81[ASN][1000 genomes]
rs62284707	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155460800-155463600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:155461000-155464400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155461200-155464200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
6	chr3:155461400-155463600	Active TSS	Pancreas	Pancrea
7	chr3:155461400-155463800	Active TSS	Gastric	stomach
8	chr3:155461400-155463800	Active TSS	Right Ventricle	heart
9	chr3:155461400-155463800	Active TSS	A549	lung
10	chr3:155461400-155463800	Active TSS	NHLF	lung
11	chr3:155461400-155464000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:155461400-155464000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:155461400-155464000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:155461400-155464000	Active TSS	Right Atrium	heart
15	chr3:155461400-155464200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:155461400-155464200	Active TSS	Brain Angular Gyrus	brain
17	chr3:155461400-155464200	Active TSS	Brain Cingulate Gyrus	brain
18	chr3:155461600-155463400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:155461600-155463400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr3:155461600-155463400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr3:155461600-155463600	Active TSS	Brain Substantia Nigra	brain
22	chr3:155461600-155463600	Active TSS	Colon Smooth Muscle	Colon
23	chr3:155461600-155463600	Bivalent/Poised TSS	Thymus	Thymus
24	chr3:155461600-155463800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:155461600-155463800	Active TSS	Aorta	Aorta
26	chr3:155461600-155463800	Active TSS	Ovary	ovary
27	chr3:155461600-155464000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:155461600-155464000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:155461600-155464000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:155461600-155464000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr3:155461600-155464200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:155461600-155464400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr3:155461800-155463400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:155461800-155463400	Flanking Active TSS	Osteobl	bone
35	chr3:155461800-155463800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:155461800-155463800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr3:155461800-155463800	Active TSS	Brain Anterior Caudate	brain
38	chr3:155462000-155463400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr3:155462000-155463800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
40	chr3:155462200-155463400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr3:155462200-155463600	Active TSS	NH-A	brain
42	chr3:155462200-155463800	Active TSS	Brain Hippocampus Middle	brain
43	chr3:155462400-155463600	Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:155462400-155463800	Active TSS	Stomach Mucosa	stomach
45	chr3:155462600-155463800	Active TSS	Duodenum Mucosa	Duodenum
46	chr3:155462600-155464000	Bivalent/Poised TSS	Fetal Kidney	kidney
47	chr3:155462600-155464000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:155462600-155464200	Active TSS	Fetal Brain Female	brain
49	chr3:155462800-155463400	Active TSS	HepG2	liver
50	chr3:155462800-155464000	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links