Variant report

Variant	rs352141
Chromosome Location	chr3:52267118-52267119
allele	C/G
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	CTCF	chr3:52266980-52267130	HRE	kidney:	n/a	n/a
2	CTCF	chr3:52266980-52267130	A549	lung:	n/a	n/a
3	CTCF	chr3:52266980-52267130	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr3:52266808-52267180	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:52266956-52267138	GM12878	blood:	n/a	n/a
6	RAD21	chr3:52266707-52267264	H1-hESC	embryonic stem cell:	n/a	chr3:52267083-52267096
7	CTCF	chr3:52266960-52267230	GM12874	blood:	n/a	n/a
8	RAD21	chr3:52266854-52267160	H1-hESC	embryonic stem cell:	n/a	chr3:52267083-52267096
9	RAD21	chr3:52266857-52267197	H1-hESC	embryonic stem cell:	n/a	chr3:52267083-52267096
10	CTCF	chr3:52266802-52267177	K562	blood:	n/a	n/a
11	CTCF	chr3:52266920-52267130	GM06990	blood:	n/a	n/a
12	RAD21	chr3:52266873-52267171	SK-N-SH_RA	brain:	n/a	chr3:52267083-52267096
13	CTCF	chr3:52266980-52267130	HFF-Myc	foreskin:	n/a	n/a
14	CTCF	chr3:52266980-52267130	HPAF	blood vessel:	n/a	n/a
15	RAD21	chr3:52266899-52267150	HepG2	liver:	n/a	chr3:52267083-52267096
16	CTCF	chr3:52266869-52267180	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr3:52267040-52267190	HA-sp	spinal cord:	n/a	n/a
18	CTCF	chr3:52266980-52267130	HAc	cerebellar:	n/a	n/a
19	CTCF	chr3:52267040-52267190	A549	lung:	n/a	n/a
20	CTCF	chr3:52267060-52267210	GM12878	blood:	n/a	n/a
21	RAD21	chr3:52266945-52267156	Hela-S3	cervix:	n/a	chr3:52267083-52267096
22	RAD21	chr3:52266882-52267118	HepG2	liver:	n/a	chr3:52267083-52267096
23	CTCF	chr3:52266980-52267130	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
2	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
3	chr3:52266609..52268371-chr3:52308578..52311025,2	MCF-7	breast:
4	chr3:52264055..52267306-chr3:52309351..52312799,8	MCF-7	breast:
5	chr3:52262375..52268246-chr3:52270366..52274345,8	K562	blood:

Variant related genes	Relation type
TWF2	TF binding region
ENSG00000173366	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs104902	0.92[ASN][1000 genomes]
rs123598	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123603	0.83[EUR][1000 genomes]
rs13065677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13071708	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13076508	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13089892	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13091360	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13093555	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096571	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098856	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164636	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164637	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2109557	0.82[AMR][1000 genomes]
rs34181173	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34332947	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34385735	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34551211	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34628357	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34827613	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35130772	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352144	0.93[EUR][1000 genomes]
rs352173	0.84[ASN][1000 genomes]
rs353545	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353548	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35982798	0.85[EUR][1000 genomes]
rs3755810	0.82[AMR][1000 genomes]
rs3796342	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs419050	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419604	0.82[AMR][1000 genomes]
rs419752	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4687614	0.84[AMR][1000 genomes]
rs498778	0.82[AMR][1000 genomes]
rs575476	0.82[AMR][1000 genomes]
rs61734640	0.85[EUR][1000 genomes]
rs6795333	0.82[AMR][1000 genomes]
rs71297391	0.85[EUR][1000 genomes]
rs71297394	0.85[EUR][1000 genomes]
rs71297395	0.85[EUR][1000 genomes]
rs71297396	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
3	chr3:52255000-52268600	Weak transcription	Right Atrium	heart
4	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:52259600-52268200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:52261000-52269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
8	chr3:52261400-52269000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:52261400-52269600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:52261600-52267200	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:52261600-52270600	Strong transcription	NHEK	skin
15	chr3:52261800-52267200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52261800-52267800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:52261800-52269400	Strong transcription	Brain Germinal Matrix	brain
18	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:52261800-52270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:52262000-52269200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:52262400-52269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:52262400-52269800	Strong transcription	Osteobl	bone
25	chr3:52262400-52270000	Strong transcription	NHLF	lung
26	chr3:52262800-52268600	Strong transcription	Ovary	ovary
27	chr3:52263000-52269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:52263200-52269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52264200-52271400	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr3:52264600-52270000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:52264800-52267800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:52264800-52270600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:52265000-52269400	Weak transcription	Hela-S3	cervix
34	chr3:52265000-52270400	Weak transcription	K562	blood
35	chr3:52265000-52272000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:52265200-52267400	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr3:52265200-52267600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:52265200-52267600	Genic enhancers	Fetal Thymus	thymus
39	chr3:52265200-52267600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
40	chr3:52265200-52269400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:52265200-52270400	Weak transcription	HSMMtube	muscle
42	chr3:52265200-52270800	Weak transcription	HUVEC	blood vessel
43	chr3:52265400-52267200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
44	chr3:52265400-52269200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:52265400-52269200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:52265400-52269600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:52265400-52269800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:52265400-52270800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:52265400-52271800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:52265600-52267600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links