Variant report

Variant	rs2629450
Chromosome Location	chr12:56615263-56615264
allele	A/C
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	SIN3A	chr12:56614664-56616490	H1-hESC	embryonic stem cell:	n/a	chr12:56615801-56615810
2	POLR2A	chr12:56614864-56616393	HUVEC	blood vessel:	n/a	n/a
3	GABPA	chr12:56614409-56616328	SK-N-SH	brain:	n/a	chr12:56615521-56615535 chr12:56615717-56615726 chr12:56615524-56615538 chr12:56615524-56615533 chr12:56615524-56615535
4	WRNIP1	chr12:56615155-56615312	GM12878	blood:	n/a	n/a
5	SIX5	chr12:56615079-56616402	A549	lung:	n/a	n/a
6	POLR2A	chr12:56614398-56616652	HUVEC	blood vessel:	n/a	n/a
7	SREBP1	chr12:56614876-56616403	GM12878	blood:	n/a	n/a
8	JUND	chr12:56615121-56615316	K562	blood:	n/a	n/a
9	PBX3	chr12:56615077-56615317	GM12878	blood:	n/a	n/a
10	MAX	chr12:56614854-56616537	A549	lung:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56616487-56616496 chr12:56615148-56615158
11	POLR2A	chr12:56615260-56616681	U87	brain:	n/a	n/a
12	TEAD4	chr12:56614551-56615290	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr12:56614682-56616474	ECC-1	luminal epithelium:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56615148-56615158
14	POLR2A	chr12:56615242-56615268	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:56614874-56618402	HepG2	liver:	n/a	n/a
16	MAX	chr12:56614469-56616122	NB4	blood:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56615148-56615158
17	YY1	chr12:56614825-56616213	ECC-1	luminal epithelium:	n/a	chr12:56616160-56616171 chr12:56616162-56616171
18	HMGN3	chr12:56615136-56616217	K562	blood:	n/a	n/a
19	MAX	chr12:56614549-56616342	ECC-1	luminal epithelium:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56615148-56615158
20	SP1	chr12:56614883-56616493	A549	lung:	n/a	chr12:56615761-56615772 chr12:56615715-56615726 chr12:56615716-56615725 chr12:56615147-56615159 chr12:56615289-56615303 chr12:56615459-56615468 chr12:56615147-56615159 chr12:56615717-56615726 chr12:56615762-56615771 chr12:56615716-56615726 chr12:56615716-56615726 chr12:56615715-56615727 chr12:56615460-56615469 chr12:56615715-56615727 chr12:56615148-56615157 chr12:56614920-56614934
21	HCFC1	chr12:56614337-56616182	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:56614415-56616400	HL-60	blood:	n/a	n/a
23	MAX	chr12:56615200-56616526	K562	blood:	n/a	chr12:56615716-56615726 chr12:56616487-56616496
24	POLR2A	chr12:56614755-56615432	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:56615260-56616522	U87	brain:	n/a	n/a
26	POLR2A	chr12:56615086-56616344	MCF-7	breast:	n/a	n/a
27	PBX3	chr12:56614559-56616047	SK-N-SH	brain:	n/a	chr12:56614862-56614871
28	CHD1	chr12:56615026-56615453	GM12878	blood:	n/a	n/a
29	MXI1	chr12:56615013-56615901	Hela-S3	cervix:	n/a	n/a
30	ZNF263	chr12:56614680-56616155	HEK293-T-REx	kidney:	n/a	chr12:56615204-56615213 chr12:56615487-56615496 chr12:56614923-56614932
31	POLR2A	chr12:56615039-56616199	Hela-S3	cervix:	n/a	n/a
32	SMARCB1	chr12:56615004-56616221	Hela-S3	cervix:	n/a	n/a
33	CREB1	chr12:56615011-56616246	GM12878	blood:	n/a	n/a
34	MTA3	chr12:56615211-56616498	GM12878	blood:	n/a	n/a
35	JUND	chr12:56615020-56616027	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr12:56614571-56616386	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr12:56614755-56616447	U87	brain:	n/a	n/a
38	MAZ	chr12:56614885-56615365	HepG2	liver:	n/a	chr12:56614919-56614929 chr12:56615148-56615158
39	POLR2A	chr12:56614522-56616401	IMR90	lung:	n/a	n/a
40	TCF12	chr12:56614672-56616396	ECC-1	luminal epithelium:	n/a	n/a
41	ZBTB7A	chr12:56614770-56615892	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr12:56614749-56616516	U87	brain:	n/a	n/a
43	POLR2A	chr12:56614497-56616422	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr12:56614505-56616256	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr12:56614929-56616405	Hela-S3	cervix:	n/a	n/a
46	TCF12	chr12:56614594-56616314	ECC-1	luminal epithelium:	n/a	n/a
47	TCF12	chr12:56615119-56616473	A549	lung:	n/a	n/a
48	GABPA	chr12:56615166-56616701	MCF-7	breast:	n/a	chr12:56615521-56615535 chr12:56615717-56615726 chr12:56615524-56615538 chr12:56615524-56615533 chr12:56615524-56615535
49	POLR2A	chr12:56614846-56616485	ProgFib	skin:	n/a	n/a
50	POLR2A	chr12:56614783-56616187	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
2	chr12:56606322..56608924-chr12:56614392..56617404,3	MCF-7	breast:
3	chr12:56614363..56617210-chr12:56726508..56729493,3	K562	blood:
4	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
5	chr12:56614513..56617977-chr12:56679402..56681953,3	K562	blood:
6	chr12:56614288..56617250-chr12:56628916..56630497,2	K562	blood:
7	chr12:56434197..56436008-chr12:56614741..56617329,2	K562	blood:
8	chr12:56546962..56549504-chr12:56614764..56616913,2	MCF-7	breast:
9	chr12:56614200..56620176-chr12:56644045..56650698,8	K562	blood:
10	chr12:56614747..56618810-chr12:56659447..56662577,5	K562	blood:
11	chr12:56615114..56616062-chr17:7591464..7592167,2	HCT-116	colon:
12	chr12:56520558..56523356-chr12:56614094..56616710,4	K562	blood:
13	chr12:56606354..56610392-chr12:56613995..56616440,4	MCF-7	breast:
14	chr12:56520093..56522899-chr12:56615142..56617287,3	MCF-7	breast:
15	chr12:56509441..56516191-chr12:56612345..56620104,13	K562	blood:
16	chr12:56614920..56617825-chr12:56620846..56625139,7	MCF-7	breast:
17	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
18	chr12:56510450..56514790-chr12:56614310..56619055,13	K562	blood:
19	chr12:56615078..56617831-chr12:56708226..56710350,2	MCF-7	breast:
20	chr12:56609459..56612925-chr12:56614221..56618096,8	MCF-7	breast:
21	chr12:56613850..56618210-chr12:56691526..56695895,7	MCF-7	breast:
22	chr12:56499013..56501029-chr12:56614482..56616399,2	K562	blood:
23	chr12:56613473..56616286-chr12:56659565..56662272,3	MCF-7	breast:
24	chr12:56473421..56475215-chr12:56613648..56616195,2	MCF-7	breast:
25	chr12:56614600..56619518-chr12:56692701..56695411,5	K562	blood:
26	chr12:56606878..56611530-chr12:56612338..56617285,8	K562	blood:
27	chr12:56519631..56523356-chr12:56615060..56618173,5	K562	blood:
28	chr12:56596803..56602914-chr12:56614556..56619492,8	MCF-7	breast:
29	chr12:56613428..56616979-chr12:56726022..56728314,3	MCF-7	breast:
30	chr12:56598444..56603105-chr12:56614822..56617186,4	K562	blood:
31	chr12:56600189..56603854-chr12:56613542..56616774,5	MCF-7	breast:
32	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
33	chr12:56613576..56617252-chr12:56649934..56653548,9	MCF-7	breast:
34	chr12:56614118..56616617-chr12:56622864..56625274,4	K562	blood:
35	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
36	chr12:56614067..56616141-chr12:56881501..56883346,2	MCF-7	breast:
37	chr12:56613899..56621490-chr12:56648204..56656770,13	K562	blood:
38	chr12:56613710..56617049-chr12:56651125..56653434,4	K562	blood:
39	chr12:56615112..56618048-chr12:56649665..56653829,3	MCF-7	breast:

Variant related genes	Relation type
RNF41	TF binding region
NABP2	TF binding region
ENSG00000062485	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000141499	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000266023	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135473	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1274298	1.00[CHD][hapmap]
rs1274494	1.00[GIH][hapmap]
rs12810816	1.00[CHD][hapmap]
rs1290898	1.00[CHD][hapmap]
rs17118313	1.00[CHD][hapmap]
rs35436573	1.00[CHD][hapmap]
rs66864435	0.90[EUR][1000 genomes]
rs7311505	0.82[EUR][1000 genomes]
rs773120	1.00[CHD][hapmap]
rs773121	1.00[CHD][hapmap]
rs773122	1.00[CHD][hapmap]
rs773643	1.00[CHD][hapmap]
rs773649	1.00[CHD][hapmap]
rs773662	1.00[CHD][hapmap]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56613800-56615400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:56613800-56615400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:56613800-56615800	Active TSS	HSMM	muscle
4	chr12:56613800-56615800	Active TSS	NHLF	lung
5	chr12:56614000-56615400	Active TSS	Right Atrium	heart
6	chr12:56614000-56615800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:56614000-56616200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:56614000-56616800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:56614200-56615400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr12:56614200-56615400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:56614200-56615400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:56614200-56615800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:56614200-56615800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:56614200-56615800	Active TSS	HSMMtube	muscle
15	chr12:56614200-56616200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:56614200-56616200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:56614200-56616200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:56614200-56616600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr12:56614400-56615400	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr12:56614400-56615400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr12:56614400-56615400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:56614400-56615800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:56614400-56616000	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:56614400-56616000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:56614400-56616000	Active TSS	NHDF-Ad	bronchial
26	chr12:56614400-56616200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr12:56614400-56616200	Active TSS	Right Ventricle	heart
28	chr12:56614400-56616400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:56614400-56616400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:56614400-56616600	Active TSS	GM12878-XiMat	blood
31	chr12:56614400-56617200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:56614400-56617200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr12:56614600-56615400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr12:56614600-56615400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr12:56614600-56615400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:56614600-56615400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:56614600-56615400	Flanking Active TSS	Liver	Liver
38	chr12:56614600-56615400	Flanking Active TSS	Fetal Thymus	thymus
39	chr12:56614600-56615600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr12:56614600-56615800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:56614600-56616200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:56614600-56616200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr12:56614600-56616200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:56614600-56616400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:56614600-56616400	Active TSS	Aorta	Aorta
46	chr12:56614600-56616400	Active TSS	Esophagus	oesophagus
47	chr12:56614600-56616400	Active TSS	Gastric	stomach
48	chr12:56614600-56616400	Active TSS	Left Ventricle	heart
49	chr12:56614600-56616400	Active TSS	Ovary	ovary
50	chr12:56614600-56619000	Active TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links