Variant report

Variant	rs113533522
Chromosome Location	chr3:142840519-142840520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCLAF1	chr3:142839701-142840519	GM12878	blood:	n/a	n/a
2	CTCF	chr3:142840142-142840551	HCT-116	colon:	n/a	n/a
3	POLR2A	chr3:142837773-142841232	GM19193	blood:	n/a	n/a
4	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
5	RAD21	chr3:142840131-142840680	A549	lung:	n/a	n/a
6	RAD21	chr3:142839731-142840584	IMR90	lung:	n/a	n/a
7	POLR2A	chr3:142837371-142841744	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
10	RAD21	chr3:142840123-142840548	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr3:142837796-142841213	GM12878	blood:	n/a	n/a
12	RAD21	chr3:142840158-142840523	A549	lung:	n/a	n/a
13	CTCF	chr3:142840125-142840535	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:142837372-142842950	GM12891	blood:	n/a	n/a
15	CTCF	chr3:142840107-142840685	HCT-116	colon:	n/a	n/a
16	CTCF	chr3:142839787-142840536	K562	blood:	n/a	n/a
17	CTCF	chr3:142839760-142840566	IMR90	lung:	n/a	n/a
18	CTCF	chr3:142839696-142840741	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:142837824-142840822	GM12878	blood:	n/a	n/a
20	E2F6	chr3:142838899-142840803	H1-hESC	embryonic stem cell:	n/a	chr3:142838914-142838924 chr3:142838911-142838921 chr3:142839536-142839546 chr3:142839574-142839584 chr3:142839630-142839639 chr3:142839543-142839552 chr3:142838917-142838927
21	CHD2	chr3:142839790-142840529	GM12878	blood:	n/a	n/a
22	CTCF	chr3:142840071-142840548	A549	lung:	n/a	n/a
23	MAX	chr3:142839884-142840531	A549	lung:	n/a	n/a
24	POLR2A	chr3:142839825-142840623	GM12878	blood:	n/a	n/a
25	MAX	chr3:142839714-142840627	GM12878	blood:	n/a	n/a
26	USF2	chr3:142840010-142840644	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr3:142839762-142840614	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr3:142840093-142840541	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr3:142839652-142840711	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr3:142840156-142840604	SK-N-SH_RA	brain:	n/a	n/a
31	RUNX3	chr3:142837697-142840604	GM12878	blood:	n/a	n/a
32	PAX5	chr3:142840067-142840555	GM12878	blood:	n/a	n/a
33	CTCF	chr3:142839743-142840569	GM12892	blood:	n/a	n/a
34	CBX3	chr3:142840160-142840831	K562	blood:	n/a	n/a
35	ZNF143	chr3:142839847-142840623	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:142839539-142840864	H1-hESC	embryonic stem cell:	n/a	n/a
37	JUND	chr3:142840094-142840573	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:142837700-142841323	K562	blood:	n/a	n/a
39	POLR2A	chr3:142840476-142840527	MCF-7	breast:	n/a	n/a
40	CTCF	chr3:142840106-142840528	ProgFib	skin:	n/a	n/a
41	POU2F2	chr3:142840067-142840592	GM12891	blood:	n/a	n/a
42	BHLHE40	chr3:142839766-142840539	GM12878	blood:	n/a	n/a
43	CTCF	chr3:142840160-142840522	NHEK	skin:	n/a	n/a
44	POLR2A	chr3:142840452-142840654	MCF-7	breast:	n/a	n/a
45	E2F6	chr3:142839578-142840716	H1-hESC	embryonic stem cell:	n/a	chr3:142839630-142839639
46	RAD21	chr3:142840035-142840609	H1-hESC	embryonic stem cell:	n/a	n/a
47	SMC3	chr3:142839585-142840631	SK-N-SH	brain:	n/a	n/a
48	POU2F2	chr3:142840140-142840796	GM12891	blood:	n/a	n/a
49	CTCF	chr3:142840167-142840537	K562	blood:	n/a	n/a
50	ZNF143	chr3:142838980-142840529	GM12878	blood:	n/a	chr3:142839542-142839552

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142839497..142841574-chr3:143081300..143083347,2	K562	blood:
2	chr3:142777135..142778996-chr3:142838578..142841035,2	K562	blood:
3	chr3:142729466..142731298-chr3:142840071..142842956,2	K562	blood:
4	chr3:142795942..142798929-chr3:142838470..142841083,3	K562	blood:
5	chr3:142839097..142841882-chr3:143060810..143062990,2	K562	blood:
6	chr3:142729466..142732055-chr3:142838748..142841571,2	K562	blood:
7	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
8	chr3:142839303..142841374-chr3:143036089..143037614,2	K562	blood:
9	chr3:142839696..142842108-chr3:143048440..143050143,2	K562	blood:
10	chr3:142838518..142840970-chr3:143064617..143066302,2	K562	blood:
11	chr3:142839800..142841734-chr3:142873166..142874850,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241679	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000240012	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3438597	chr3:142838687-142841235	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
8	esv3421903	chr3:142839312-142842010	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142837200-142840600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:142837400-142840600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:142837600-142840600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:142837600-142840600	Active TSS	Primary T cells from cord blood	blood
5	chr3:142837600-142840600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:142837600-142840600	Active TSS	NHLF	lung
7	chr3:142837600-142840600	Active TSS	Osteobl	bone
8	chr3:142837600-142840800	Active TSS	Brain Anterior Caudate	brain
9	chr3:142837600-142840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:142837600-142841000	Active TSS	HSMM	muscle
11	chr3:142837600-142841200	Active TSS	Brain Angular Gyrus	brain
12	chr3:142837800-142840600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:142837800-142840600	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:142837800-142843400	Active TSS	Fetal Kidney	kidney
15	chr3:142838000-142840600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:142838800-142840600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr3:142838800-142840800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:142838800-142840800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr3:142839000-142840600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
20	chr3:142839200-142840600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:142839200-142840600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:142839200-142840600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
23	chr3:142839200-142845800	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr3:142839200-142847200	Transcr. at gene 5' and 3'	Fetal Lung	lung
25	chr3:142839400-142840600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:142839400-142840800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
27	chr3:142839400-142841600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:142839600-142840600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr3:142839600-142840800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr3:142839600-142841600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:142839600-142843200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr3:142839800-142840600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr3:142839800-142840600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr3:142839800-142840600	Flanking Bivalent TSS/Enh	Placenta	Placenta
35	chr3:142839800-142840600	Flanking Active TSS	NH-A	brain
36	chr3:142839800-142841000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr3:142840000-142840600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr3:142840000-142840600	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr3:142840000-142840600	Active TSS	Fetal Brain Female	brain
40	chr3:142840000-142841000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:142840000-142841800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:142840200-142840600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr3:142840200-142840600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:142840200-142840600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:142840200-142840600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:142840200-142840600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr3:142840200-142840600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
48	chr3:142840200-142840600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
49	chr3:142840200-142840600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
50	chr3:142840200-142840600	Transcr. at gene 5' and 3'	Spleen	Spleen

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