Variant report

Variant	rs2629449
Chromosome Location	chr12:56615907-56615908
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	KAP1	chr12:56615578-56616077	U2OS	brain:	n/a	n/a
2	POLR2A	chr12:56615425-56616497	PBDE	blood:	n/a	n/a
3	STAT1	chr12:56615542-56616067	GM12878	blood:	n/a	chr12:56615854-56615861 chr12:56615630-56615642
4	SIN3A	chr12:56614664-56616490	H1-hESC	embryonic stem cell:	n/a	chr12:56615801-56615810
5	POLR2A	chr12:56614864-56616393	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:56615284-56616553	MCF-7	breast:	n/a	n/a
7	CHD1	chr12:56615673-56616293	GM12878	blood:	n/a	n/a
8	SP1	chr12:56615382-56616552	A549	lung:	n/a	chr12:56615761-56615772 chr12:56615715-56615726 chr12:56615716-56615725 chr12:56615459-56615468 chr12:56615717-56615726 chr12:56615762-56615771 chr12:56615716-56615726 chr12:56615716-56615726 chr12:56615715-56615727 chr12:56615460-56615469 chr12:56615715-56615727
9	ZNF143	chr12:56615712-56616044	K562	blood:	n/a	n/a
10	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
11	POLR2A	chr12:56615284-56616288	MCF-7	breast:	n/a	n/a
12	YY1	chr12:56615437-56616183	A549	lung:	n/a	chr12:56616160-56616171 chr12:56616162-56616171
13	MYBL2	chr12:56615366-56616231	HepG2	liver:	n/a	n/a
14	HEY1	chr12:56615469-56616101	HepG2	liver:	n/a	n/a
15	PML	chr12:56615311-56616145	K562	blood:	n/a	n/a
16	SIX5	chr12:56615079-56616402	A549	lung:	n/a	n/a
17	RELA	chr12:56615465-56616073	GM18951	blood:	n/a	n/a
18	POLR2A	chr12:56614398-56616652	HUVEC	blood vessel:	n/a	n/a
19	SREBP1	chr12:56614876-56616403	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr12:56615541-56616040	HepG2	liver:	n/a	n/a
21	FOXA2	chr12:56615518-56615980	A549	lung:	n/a	n/a
22	RUNX3	chr12:56615412-56616398	GM12878	blood:	n/a	chr12:56616189-56616198 chr12:56615593-56615610
23	CTCF	chr12:56615797-56615910	Lung_OC	lung:	n/a	n/a
24	NFIC	chr12:56615615-56616105	GM12878	blood:	n/a	n/a
25	GABPA	chr12:56615338-56616371	A549	lung:	n/a	chr12:56615521-56615535 chr12:56615717-56615726 chr12:56615524-56615538 chr12:56615524-56615533 chr12:56615524-56615535
26	MYC	chr12:56615649-56616125	MCF10A-Er-Src	breast:	n/a	chr12:56615716-56615726
27	JUND	chr12:56615519-56616281	K562	blood:	n/a	n/a
28	RCOR1	chr12:56615856-56616404	K562	blood:	n/a	n/a
29	POLR2A	chr12:56615417-56616162	HEK293	kidney:	n/a	n/a
30	MAX	chr12:56614854-56616537	A549	lung:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56616487-56616496 chr12:56615148-56615158
31	POLR2A	chr12:56615260-56616681	U87	brain:	n/a	n/a
32	CHD2	chr12:56615547-56615997	Hela-S3	cervix:	n/a	n/a
33	PML	chr12:56615430-56616071	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:56615491-56616136	GM12878	blood:	n/a	n/a
35	REST	chr12:56615453-56616473	K562	blood:	n/a	chr12:56615800-56615810 chr12:56615475-56615488 chr12:56616082-56616102 chr12:56615716-56615729
36	MAX	chr12:56614682-56616474	ECC-1	luminal epithelium:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56615148-56615158
37	SPI1	chr12:56615432-56616136	HL-60	blood:	n/a	n/a
38	CEBPB	chr12:56615475-56616209	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:56615463-56616114	GM12891	blood:	n/a	n/a
40	POU2F2	chr12:56615649-56616155	GM12891	blood:	n/a	chr12:56615720-56615732
41	MYC	chr12:56615591-56616683	K562	blood:	n/a	chr12:56615716-56615726 chr12:56616487-56616496
42	TAF1	chr12:56615735-56615952	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:56615435-56616216	GM15510	blood:	n/a	n/a
44	POLR2A	chr12:56614874-56618402	HepG2	liver:	n/a	n/a
45	MAX	chr12:56614469-56616122	NB4	blood:	n/a	chr12:56614919-56614929 chr12:56615716-56615726 chr12:56615148-56615158
46	POLR2A	chr12:56615381-56616075	SK-N-MC	brain:	n/a	n/a
47	YY1	chr12:56614825-56616213	ECC-1	luminal epithelium:	n/a	chr12:56616160-56616171 chr12:56616162-56616171
48	HMGN3	chr12:56615136-56616217	K562	blood:	n/a	n/a
49	CTCF	chr12:56615668-56615958	Spleen_OC	spleen:	n/a	n/a
50	MYC	chr12:56615779-56616081	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
2	chr12:56583290..56583861-chr12:56615727..56616256,2	K562	blood:
3	chr12:56606322..56608924-chr12:56614392..56617404,3	MCF-7	breast:
4	chr12:56614363..56617210-chr12:56726508..56729493,3	K562	blood:
5	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
6	chr12:56614513..56617977-chr12:56679402..56681953,3	K562	blood:
7	chr12:56615744..56616435-chr7:86781329..86782188,2	NB4	blood:
8	chr12:56614288..56617250-chr12:56628916..56630497,2	K562	blood:
9	chr12:56434197..56436008-chr12:56614741..56617329,2	K562	blood:
10	chr12:56582602..56584136-chr12:56615794..56617313,2	K562	blood:
11	chr12:56546962..56549504-chr12:56614764..56616913,2	MCF-7	breast:
12	chr12:56614200..56620176-chr12:56644045..56650698,8	K562	blood:
13	chr12:56614747..56618810-chr12:56659447..56662577,5	K562	blood:
14	chr12:56615764..56616333-chr2:38977794..38978848,3	Hela-S3	cervix:
15	chr12:56615114..56616062-chr17:7591464..7592167,2	HCT-116	colon:
16	chr12:56520558..56523356-chr12:56614094..56616710,4	K562	blood:
17	chr12:56606354..56610392-chr12:56613995..56616440,4	MCF-7	breast:
18	chr12:56520093..56522899-chr12:56615142..56617287,3	MCF-7	breast:
19	chr12:56509441..56516191-chr12:56612345..56620104,13	K562	blood:
20	chr12:56614920..56617825-chr12:56620846..56625139,7	MCF-7	breast:
21	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
22	chr12:56510450..56514790-chr12:56614310..56619055,13	K562	blood:
23	chr12:56615078..56617831-chr12:56708226..56710350,2	MCF-7	breast:
24	chr12:56543805..56547677-chr12:56615744..56618519,4	MCF-7	breast:
25	chr12:56609459..56612925-chr12:56614221..56618096,8	MCF-7	breast:
26	chr12:56613850..56618210-chr12:56691526..56695895,7	MCF-7	breast:
27	chr12:56499013..56501029-chr12:56614482..56616399,2	K562	blood:
28	chr12:56613473..56616286-chr12:56659565..56662272,3	MCF-7	breast:
29	chr12:56473421..56475215-chr12:56613648..56616195,2	MCF-7	breast:
30	chr12:56614600..56619518-chr12:56692701..56695411,5	K562	blood:
31	chr12:56606878..56611530-chr12:56612338..56617285,8	K562	blood:
32	chr1:17231195..17231948-chr12:56615798..56616665,2	Hela-S3	cervix:
33	chr12:56519631..56523356-chr12:56615060..56618173,5	K562	blood:
34	chr12:56596803..56602914-chr12:56614556..56619492,8	MCF-7	breast:
35	chr12:56613428..56616979-chr12:56726022..56728314,3	MCF-7	breast:
36	chr12:56598444..56603105-chr12:56614822..56617186,4	K562	blood:
37	chr12:56600189..56603854-chr12:56613542..56616774,5	MCF-7	breast:
38	chr12:56582602..56584894-chr12:56615504..56618371,3	K562	blood:
39	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
40	chr12:56613576..56617252-chr12:56649934..56653548,9	MCF-7	breast:
41	chr12:56614118..56616617-chr12:56622864..56625274,4	K562	blood:
42	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
43	chr12:56615624..56617857-chr12:56693691..56696506,3	K562	blood:
44	chr12:56509088..56512395-chr12:56615837..56618663,6	MCF-7	breast:
45	chr12:56614067..56616141-chr12:56881501..56883346,2	MCF-7	breast:
46	chr12:56613899..56621490-chr12:56648204..56656770,13	K562	blood:
47	chr12:56613710..56617049-chr12:56651125..56653434,4	K562	blood:
48	chr12:56615112..56618048-chr12:56649665..56653829,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF41-1	chr12:56615889-56616114	ucscGeneNc_uc001sqo_1

Variant related genes	Relation type
RNF41	TF binding region
NABP2	TF binding region
ENSG00000135473	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135164	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000141499	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000224046	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000266023	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000135423	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10747762	0.91[AMR][1000 genomes]
rs11171774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11575218	1.00[MEX][hapmap]
rs1274501	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1619653	1.00[MEX][hapmap]
rs1689507	1.00[MEX][hapmap]
rs17118576	1.00[MEX][hapmap]
rs1995742	1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs2066811	0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs2450101	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2450104	0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456445	1.00[MEX][hapmap]
rs2629445	1.00[MEX][hapmap]
rs35382885	1.00[MEX][hapmap]
rs4759219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs705706	1.00[MEX][hapmap]
rs7301099	0.91[ASW][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs7397453	0.87[AFR][1000 genomes]
rs773644	0.91[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs773647	0.81[AFR][1000 genomes];1.00[AMR][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	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	chr12:56614000-56616200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:56614000-56616800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56614200-56616200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56614200-56616200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:56614200-56616200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:56614200-56616600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:56614400-56616000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:56614400-56616000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:56614400-56616000	Active TSS	NHDF-Ad	bronchial
10	chr12:56614400-56616200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:56614400-56616200	Active TSS	Right Ventricle	heart
12	chr12:56614400-56616400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:56614400-56616400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:56614400-56616600	Active TSS	GM12878-XiMat	blood
15	chr12:56614400-56617200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:56614400-56617200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:56614600-56616200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:56614600-56616200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:56614600-56616200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:56614600-56616400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:56614600-56616400	Active TSS	Aorta	Aorta
22	chr12:56614600-56616400	Active TSS	Esophagus	oesophagus
23	chr12:56614600-56616400	Active TSS	Gastric	stomach
24	chr12:56614600-56616400	Active TSS	Left Ventricle	heart
25	chr12:56614600-56616400	Active TSS	Ovary	ovary
26	chr12:56614600-56619000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:56614800-56616000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:56614800-56616200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:56614800-56616200	Active TSS	Fetal Intestine Large	intestine
30	chr12:56614800-56616400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:56614800-56616400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:56614800-56616400	Active TSS	K562	blood
33	chr12:56614800-56616600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr12:56614800-56616600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr12:56614800-56616800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:56615000-56616000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:56615000-56616000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:56615000-56616000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:56615000-56616000	Active TSS	Brain Cingulate Gyrus	brain
40	chr12:56615000-56616000	Active TSS	Brain Germinal Matrix	brain
41	chr12:56615000-56616000	Active TSS	Fetal Brain Male	brain
42	chr12:56615000-56616000	Active TSS	Fetal Intestine Small	intestine
43	chr12:56615000-56616000	Active TSS	Fetal Stomach	stomach
44	chr12:56615000-56616000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr12:56615000-56616000	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:56615000-56616000	Active TSS	HMEC	breast
47	chr12:56615000-56616000	Active TSS	Osteobl	bone
48	chr12:56615000-56616200	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr12:56615000-56616200	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr12:56615000-56616200	Active TSS	Brain Angular Gyrus	brain

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