Variant report

Variant	rs7331851
Chromosome Location	chr13:49154351-49154352
allele	G/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	RAD21	chr13:49154293-49154773	SK-N-SH_RA	brain:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
2	CTCF	chr13:49154302-49154680	T-47D	breast:	n/a	chr13:49154517-49154535
3	POLR2A	chr13:49152429-49154926	GM12891	blood:	n/a	n/a
4	RAD21	chr13:49154197-49154812	HepG2	liver:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
5	CTCF	chr13:49154343-49154742	K562	blood:	n/a	chr13:49154517-49154535
6	RAD21	chr13:49154313-49154753	GM12878	blood:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
7	RAD21	chr13:49154330-49154777	H1-hESC	embryonic stem cell:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
8	SMC3	chr13:49154318-49154731	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr13:49154248-49154771	MCF-7	breast:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
10	CTCF	chr13:49154296-49154854	HCT-116	colon:	n/a	chr13:49154517-49154535
11	SMC3	chr13:49154328-49154763	HepG2	liver:	n/a	n/a
12	RAD21	chr13:49154322-49154711	SK-N-SH_RA	brain:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
13	RAD21	chr13:49153604-49155108	SK-N-SH	brain:	n/a	chr13:49153823-49153837 chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
14	RAD21	chr13:49154324-49154792	HCT-116	colon:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
15	CTCF	chr13:49154216-49154967	A549	lung:	n/a	chr13:49154517-49154535
16	CTCF	chr13:49154329-49154758	IMR90	lung:	n/a	chr13:49154517-49154535
17	RAD21	chr13:49154324-49154752	HepG2	liver:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
18	RAD21	chr13:49154251-49154774	H1-hESC	embryonic stem cell:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
19	ZNF384	chr13:49153264-49154849	GM12878	blood:	n/a	n/a
20	CTCF	chr13:49154258-49154706	HepG2	liver:	n/a	chr13:49154517-49154535
21	CTCF	chr13:49154340-49154822	GM12878	blood:	n/a	chr13:49154517-49154535
22	CTCF	chr13:49154280-49154682	H1-hESC	embryonic stem cell:	n/a	chr13:49154517-49154535
23	CTCF	chr13:49154308-49154660	HCT-116	colon:	n/a	chr13:49154517-49154535
24	RAD21	chr13:49154330-49154732	Hela-S3	cervix:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
25	RAD21	chr13:49154300-49154694	GM12878	blood:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
26	RAD21	chr13:49154328-49154748	A549	lung:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
27	FOXA1	chr13:49154260-49154682	HepG2	liver:	n/a	n/a
28	ZNF384	chr13:49154240-49154753	K562	blood:	n/a	n/a
29	SMC3	chr13:49152753-49154802	GM12878	blood:	n/a	n/a
30	CTCF	chr13:49154327-49154777	MCF-7	breast:	n/a	chr13:49154517-49154535
31	RAD21	chr13:49154258-49154830	IMR90	lung:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
32	RAD21	chr13:49154328-49154693	GM12878	blood:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
33	CTCF	chr13:49154277-49155091	SK-N-SH	brain:	n/a	chr13:49154517-49154535
34	MAX	chr13:49154295-49154503	GM12878	blood:	n/a	n/a
35	CTCF	chr13:49154317-49154809	MCF-7	breast:	n/a	chr13:49154517-49154535
36	SMC3	chr13:49153653-49154942	SK-N-SH	brain:	n/a	n/a
37	RAD21	chr13:49154276-49154812	ECC-1	luminal epithelium:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
38	RAD21	chr13:49154298-49154837	HCT-116	colon:	n/a	chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48806307..48808548-chr13:49152200..49154470,2	MCF-7	breast:
2	chr13:48908843..48909363-chr13:49153698..49154640,2	MCF-7	breast:

Variant related genes	Relation type
LINC00462	TF binding region
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1926596	0.83[ASN][1000 genomes]
rs198577	0.89[JPT][hapmap]
rs2274400	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs28414460	0.83[ASN][1000 genomes]
rs28646083	0.83[ASN][1000 genomes]
rs403390	0.81[JPT][hapmap]
rs4151601	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7319339	1.00[EUR][1000 genomes]
rs7329865	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7987935	0.83[ASN][1000 genomes]
rs7995216	1.00[CEU][hapmap]
rs7996186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9331959	0.83[ASN][1000 genomes]
rs9331965	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9331973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9332054	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49146800-49157400	Weak transcription	HSMMtube	muscle
3	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
4	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
6	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr13:49152400-49155000	Enhancers	Dnd41	blood
10	chr13:49152600-49154800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:49152600-49155000	Enhancers	Brain Anterior Caudate	brain
12	chr13:49152600-49155400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:49152800-49154400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:49152800-49155000	Enhancers	HepG2	liver
17	chr13:49152800-49155200	Enhancers	Brain Hippocampus Middle	brain
18	chr13:49152800-49155400	Enhancers	HMEC	breast
19	chr13:49153000-49154800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr13:49153200-49154400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:49153200-49154600	Enhancers	Primary B cells from peripheral blood	blood
22	chr13:49153200-49154800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr13:49153200-49154800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr13:49153200-49155000	Enhancers	Stomach Mucosa	stomach
25	chr13:49153200-49155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:49153400-49154600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:49153400-49154800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr13:49153400-49155000	Enhancers	Brain Cingulate Gyrus	brain
29	chr13:49153400-49158200	Weak transcription	Fetal Lung	lung
30	chr13:49153600-49154800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr13:49153600-49154800	Enhancers	Liver	Liver
32	chr13:49153600-49155000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr13:49153800-49154400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:49153800-49154800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr13:49153800-49154800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:49153800-49154800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr13:49153800-49155000	Enhancers	Brain Substantia Nigra	brain
38	chr13:49154000-49154600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr13:49154000-49154600	Enhancers	Primary B cells from cord blood	blood
40	chr13:49154000-49154600	Weak transcription	Small Intestine	intestine
41	chr13:49154000-49155000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr13:49154000-49155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:49154000-49156800	Enhancers	GM12878-XiMat	blood
44	chr13:49154000-49158000	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:49154000-49158800	Weak transcription	Right Atrium	heart
46	chr13:49154000-49159000	Weak transcription	Colonic Mucosa	Colon
47	chr13:49154000-49159000	Weak transcription	Esophagus	oesophagus
48	chr13:49154000-49159000	Weak transcription	Left Ventricle	heart
49	chr13:49154000-49159000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr13:49154000-49159000	Weak transcription	Spleen	Spleen

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