Variant report

Variant	rs10880961
Chromosome Location	chr12:46765228-46765229
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	EP300	chr12:46764946-46765397	K562	blood:	n/a	chr12:46765223-46765239 chr12:46765193-46765209
2	CTCF	chr12:46765180-46765330	HAc	cerebellar:	n/a	chr12:46765223-46765236
3	RCOR1	chr12:46764817-46766002	Hela-S3	cervix:	n/a	n/a
4	RELA	chr12:46764845-46765930	GM15510	blood:	n/a	n/a
5	NR3C1	chr12:46764992-46765845	A549	lung:	n/a	chr12:46765115-46765133
6	RCOR1	chr12:46764920-46765913	K562	blood:	n/a	n/a
7	TRIM28	chr12:46764812-46765840	K562	blood:	n/a	n/a
8	CTCF	chr12:46765144-46765235	GM12891	blood:	n/a	n/a
9	CTCF	chr12:46765080-46765230	GM12868	blood:	n/a	n/a
10	USF1	chr12:46764895-46765409	GM12878	blood:	n/a	chr12:46765211-46765220 chr12:46765212-46765221 chr12:46765196-46765212 chr12:46765210-46765223 chr12:46765213-46765222 chr12:46765210-46765221 chr12:46765141-46765157 chr12:46765212-46765221 chr12:46765206-46765227
11	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
12	TAF1	chr12:46764858-46766929	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:46764668-46766879	K562	blood:	n/a	n/a
14	CTCF	chr12:46765126-46765277	GM10266	blood:	n/a	chr12:46765223-46765236
15	POLR2A	chr12:46764536-46766807	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:46764913-46765939	A549	lung:	n/a	n/a
17	STAT5A	chr12:46764718-46767011	GM12878	blood:	n/a	chr12:46765559-46765570 chr12:46765446-46765458 chr12:46765939-46765947
18	GTF2F1	chr12:46765040-46765655	H1-hESC	embryonic stem cell:	n/a	n/a
19	CCNT2	chr12:46764899-46766920	K562	blood:	n/a	chr12:46766229-46766238 chr12:46765520-46765529 chr12:46766029-46766038
20	FOXA1	chr12:46764903-46766896	HepG2	liver:	n/a	chr12:46766358-46766370
21	MYC	chr12:46764918-46767690	NB4	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
22	MYC	chr12:46765104-46765576	MCF-7	breast:	n/a	chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
23	CTCF	chr12:46765154-46765287	H1-hESC	embryonic stem cell:	n/a	chr12:46765223-46765236
24	PAX5	chr12:46765054-46765233	GM12891	blood:	n/a	n/a
25	JUND	chr12:46764013-46766842	SK-N-SH	brain:	n/a	n/a
26	EP300	chr12:46765026-46765375	SK-N-SH_RA	brain:	n/a	chr12:46765223-46765239 chr12:46765193-46765209
27	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
28	YY1	chr12:46765052-46765947	ECC-1	luminal epithelium:	n/a	chr12:46765926-46765935 chr12:46765803-46765814 chr12:46765923-46765934
29	MAX	chr12:46764982-46765602	H1-hESC	embryonic stem cell:	n/a	chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
30	USF1	chr12:46764937-46765426	SK-N-SH_RA	brain:	n/a	chr12:46765211-46765220 chr12:46765212-46765221 chr12:46765196-46765212 chr12:46765210-46765223 chr12:46765213-46765222 chr12:46765210-46765221 chr12:46765141-46765157 chr12:46765212-46765221 chr12:46765206-46765227
31	TAF1	chr12:46764776-46766057	A549	lung:	n/a	n/a
32	POLR2A	chr12:46764987-46767683	HCT-116	colon:	n/a	n/a
33	CTCF	chr12:46765180-46765330	Caco-2	colon:	n/a	chr12:46765223-46765236
34	PBX3	chr12:46764946-46766760	A549	lung:	n/a	n/a
35	SP1	chr12:46764966-46765572	H1-hESC	embryonic stem cell:	n/a	chr12:46765290-46765301 chr12:46765308-46765319
36	TAF1	chr12:46764942-46765799	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
38	NFIC	chr12:46764107-46766064	HepG2	liver:	n/a	n/a
39	REST	chr12:46764583-46767732	H1-neurons	neurons:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147 chr12:46767136-46767144
40	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
41	YY1	chr12:46764965-46765541	GM12892	blood:	n/a	n/a
42	CTCF	chr12:46765116-46765397	IMR90	lung:	n/a	chr12:46765223-46765236
43	CTCF	chr12:46765049-46765313	Spleen_OC	spleen:	n/a	chr12:46765223-46765236
44	SP1	chr12:46764816-46765586	H1-hESC	embryonic stem cell:	n/a	chr12:46765290-46765301 chr12:46765308-46765319
45	SIN3AK20	chr12:46764904-46765294	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
47	MAZ	chr12:46764964-46768004	K562	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
48	USF1	chr12:46764879-46765522	K562	blood:	n/a	chr12:46765211-46765220 chr12:46765212-46765221 chr12:46765196-46765212 chr12:46765210-46765223 chr12:46765213-46765222 chr12:46765210-46765221 chr12:46765141-46765157 chr12:46765212-46765221 chr12:46765206-46765227
49	SP1	chr12:46764683-46767225	A549	lung:	n/a	chr12:46766079-46766088 chr12:46766228-46766242 chr12:46766606-46766618 chr12:46766227-46766239 chr12:46766606-46766617 chr12:46766606-46766618 chr12:46766228-46766237 chr12:46766077-46766089 chr12:46765290-46765301 chr12:46766077-46766089 chr12:46766027-46766039 chr12:46766662-46766673 chr12:46766229-46766238 chr12:46765308-46765319 chr12:46766227-46766239 chr12:46766029-46766038 chr12:46766228-46766238 chr12:46766078-46766087
50	POLR2A	chr12:46764638-46766115	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46656458..46664971-chr12:46763618..46767965,19	MCF-7	breast:
2	chr1:28975051..28975554-chr12:46764902..46765803,2	Hela-S3	cervix:
3	chr12:46764326..46765231-chr5:74632235..74633154,2	Hela-S3	cervix:
4	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
5	chr12:46764846..46765685-chr16:30886301..30887230,2	Hela-S3	cervix:
6	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
7	chr12:46764834..46765754-chrX:47441193..47442019,2	Hela-S3	cervix:
8	chr12:46383804..46386112-chr12:46763445..46766511,3	MCF-7	breast:
9	chr12:46764907..46765560-chrX:47862787..47863596,2	Hela-S3	cervix:
10	chr12:46765221..46765889-chr6:27113866..27114658,2	Hela-S3	cervix:
11	chr12:46764989..46765609-chr17:1620140..1620885,2	Hela-S3	cervix:
12	chr12:46119720..46123062-chr12:46761797..46766025,4	K562	blood:
13	chr12:46119720..46122632-chr12:46763272..46766407,3	K562	blood:
14	chr12:46381426..46387093-chr12:46763754..46767064,8	MCF-7	breast:
15	chr12:46765086..46765689-chr16:70380707..70381691,2	Hela-S3	cervix:
16	chr12:46659532..46664131-chr12:46762494..46766775,7	K562	blood:
17	chr12:46764362..46765489-chrX:153626330..153627477,3	Hela-S3	cervix:
18	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:
19	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
20	chr1:101361635..101362214-chr12:46764751..46765545,2	Hela-S3	cervix:
21	chr1:17231211..17232091-chr12:46764357..46765383,3	Hela-S3	cervix:
22	chr11:65266501..65267444-chr12:46765211..46766513,3	Hela-S3	cervix:
23	chr1:16840091..16841008-chr12:46765112..46765799,2	Hela-S3	cervix:
24	chr10:121356214..121356904-chr12:46765185..46765741,2	NB4	blood:

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000258096	TF binding region
ENSG00000111371	Chromatin interaction
ENSG00000102265	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000168872	Chromatin interaction
ENSG00000113161	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000260083	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000247372	Chromatin interaction
ENSG00000186594	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000151923	Chromatin interaction
ENSG00000147118	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000162695	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10467213	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1079780	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10880953	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880959	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880960	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880966	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11183441	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1125909	0.82[AMR][1000 genomes]
rs12099669	0.82[AMR][1000 genomes]
rs12311507	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12317787	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12816358	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12816413	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1471223	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1492894	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2169030	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2307061	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2408497	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2408504	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2408505	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408506	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2408507	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2408508	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897968	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34119192	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3782904	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4238102	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4258438	0.80[AMR][1000 genomes]
rs4438106	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4547171	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4586238	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4768115	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768116	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768119	0.80[AMR][1000 genomes]
rs4768695	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768696	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768698	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768709	0.80[AMR][1000 genomes]
rs7132228	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7958774	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7960147	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961994	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7968173	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7968283	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974529	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7976280	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7979418	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7979514	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs898242	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs956910	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9668077	0.84[AMR][1000 genomes]
rs9669051	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9669381	0.81[AMR][1000 genomes]
rs9795971	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 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	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
4	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr12:46758800-46765600	Transcr. at gene 5' and 3'	A549	lung
6	chr12:46758800-46765600	Transcr. at gene 5' and 3'	Osteobl	bone
7	chr12:46758800-46766000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:46758800-46766000	Transcr. at gene 5' and 3'	NHEK	skin
9	chr12:46760400-46766200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:46760600-46766000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:46760600-46766000	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr12:46761200-46765400	Transcr. at gene 5' and 3'	Thymus	Thymus
13	chr12:46761200-46765800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr12:46761200-46766400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
15	chr12:46761600-46765600	Transcr. at gene 5' and 3'	Liver	Liver
16	chr12:46761600-46766000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
17	chr12:46761800-46765600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
18	chr12:46762000-46765600	Transcr. at gene 5' and 3'	Fetal Lung	lung
19	chr12:46762200-46767800	Active TSS	Right Ventricle	heart
20	chr12:46762400-46767000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:46763000-46765600	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
22	chr12:46763400-46767400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:46763400-46767800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:46763600-46767600	Active TSS	Ovary	ovary
25	chr12:46763600-46767600	Active TSS	Psoas Muscle	Psoas
26	chr12:46763800-46767200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:46763800-46767200	Active TSS	Fetal Intestine Small	intestine
28	chr12:46764400-46765400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:46764400-46765400	Active TSS	Brain Germinal Matrix	brain
30	chr12:46764400-46767000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:46764400-46767000	Active TSS	Fetal Intestine Large	intestine
32	chr12:46764400-46767200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr12:46764400-46767600	Active TSS	Fetal Muscle Trunk	muscle
34	chr12:46764400-46767600	Active TSS	Small Intestine	intestine
35	chr12:46764400-46767600	Active TSS	HSMMtube	muscle
36	chr12:46764400-46767800	Bivalent/Poised TSS	HepG2	liver
37	chr12:46764400-46768000	Active TSS	Lung	lung
38	chr12:46764400-46768000	Active TSS	Rectal Smooth Muscle	rectum
39	chr12:46764600-46767400	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr12:46764600-46767400	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:46764600-46767400	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr12:46764600-46767800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr12:46764600-46767800	Active TSS	Brain Anterior Caudate	brain
44	chr12:46764600-46767800	Active TSS	Colon Smooth Muscle	Colon
45	chr12:46764800-46765400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr12:46764800-46765600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:46764800-46765600	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:46764800-46765800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:46764800-46765800	ZNF genes & repeats	Fetal Brain Male	brain
50	chr12:46764800-46767000	Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links