Variant report

Variant	rs12828602
Chromosome Location	chr12:9838184-9838185
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr12:9837895-9838322	K562	blood:	n/a	n/a
2	STAT5A	chr12:9837812-9838295	K562	blood:	n/a	n/a
3	UBTF	chr12:9838044-9838244	K562	blood:	n/a	n/a
4	CCNT2	chr12:9837946-9838225	K562	blood:	n/a	n/a
5	FOXA2	chr12:9838119-9838360	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:9838138-9839045	GM12878	blood:	n/a	n/a
7	RCOR1	chr12:9837895-9838204	K562	blood:	n/a	n/a
8	EP300	chr12:9837894-9838339	K562	blood:	n/a	n/a
9	TBL1XR1	chr12:9837945-9838346	K562	blood:	n/a	n/a
10	NR2F2	chr12:9837878-9838222	K562	blood:	n/a	n/a
11	MAZ	chr12:9837990-9838219	K562	blood:	n/a	n/a
12	GATA1	chr12:9837965-9838234	PBDEFetal	blood:	n/a	n/a
13	POLR2A	chr12:9837813-9838237	K562	blood:	n/a	n/a
14	GATA1	chr12:9837719-9838425	K562	blood:	n/a	n/a
15	POLR2A	chr12:9837961-9839644	GM12892	blood:	n/a	n/a
16	TEAD4	chr12:9837799-9838302	K562	blood:	n/a	n/a
17	ZMIZ1	chr12:9837917-9838262	K562	blood:	n/a	n/a
18	POLR2A	chr12:9838153-9838671	GM12878	blood:	n/a	n/a
19	YY1	chr12:9838091-9838403	K562	blood:	n/a	n/a
20	EP300	chr12:9838009-9838205	K562	blood:	n/a	n/a
21	RCOR1	chr12:9837855-9838374	K562	blood:	n/a	n/a
22	GABPA	chr12:9837921-9838272	K562	blood:	n/a	n/a
23	ATF1	chr12:9837988-9838212	K562	blood:	n/a	n/a
24	POLR2A	chr12:9837851-9838237	K562	blood:	n/a	n/a
25	PML	chr12:9837839-9838255	K562	blood:	n/a	n/a
26	GABPA	chr12:9837929-9838276	K562	blood:	n/a	n/a
27	UBTF	chr12:9838044-9838238	K562	blood:	n/a	n/a
28	NR2F2	chr12:9837902-9838365	K562	blood:	n/a	n/a
29	POLR2A	chr12:9837939-9838259	K562	blood:	n/a	n/a
30	POLR2A	chr12:9838094-9838284	GM12878	blood:	n/a	n/a
31	YY1	chr12:9838025-9838480	K562	blood:	n/a	n/a
32	IRF1	chr12:9838004-9838194	K562	blood:	n/a	n/a
33	GATA2	chr12:9837815-9838360	K562	blood:	n/a	n/a
34	TRIM28	chr12:9837907-9838342	K562	blood:	n/a	n/a
35	CEBPB	chr12:9838162-9838220	K562	blood:	n/a	n/a
36	BHLHE40	chr12:9837992-9838297	K562	blood:	n/a	n/a
37	GATA2	chr12:9837897-9838227	K562	blood:	n/a	n/a
38	CEBPD	chr12:9837792-9838327	K562	blood:	n/a	n/a
39	GATA1	chr12:9837737-9838503	PBDE	blood:	n/a	n/a
40	POLR2A	chr12:9837874-9838295	K562	blood:	n/a	n/a
41	CEBPD	chr12:9837862-9838362	K562	blood:	n/a	n/a
42	GATA2	chr12:9837900-9838315	K562	blood:	n/a	n/a
43	TAL1	chr12:9837757-9838388	K562	blood:	n/a	n/a
44	FOXA1	chr12:9838027-9838346	HepG2	liver:	n/a	n/a
45	FOXA2	chr12:9838078-9838457	A549	lung:	n/a	n/a
46	JUND	chr12:9837903-9838239	K562	blood:	n/a	n/a
47	YY1	chr12:9838154-9838387	GM12878	blood:	n/a	n/a
48	MAX	chr12:9837984-9838367	K562	blood:	n/a	n/a
49	TEAD4	chr12:9837820-9838388	K562	blood:	n/a	n/a
50	MYC	chr12:9838015-9838216	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
CLEC2D	TF binding region

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1008611	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10466762	1.00[JPT][hapmap]
rs10743820	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10743821	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs10743822	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10772005	1.00[JPT][hapmap]
rs10772006	1.00[JPT][hapmap]
rs10772060	1.00[CHB][hapmap]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844350	1.00[JPT][hapmap]
rs10844351	1.00[JPT][hapmap]
rs10844359	1.00[JPT][hapmap]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844449	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844457	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844476	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844780	1.00[JPT][hapmap]
rs11052234	1.00[JPT][hapmap]
rs11052241	1.00[JPT][hapmap]
rs11052254	1.00[JPT][hapmap]
rs11052303	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052304	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052305	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052366	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052367	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052434	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052718	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11052785	0.84[ASN][1000 genomes]
rs11053051	1.00[JPT][hapmap]
rs11519377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11524523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12309762	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12320830	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366653	1.00[JPT][hapmap]
rs12368445	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs12371982	1.00[AFR][1000 genomes]
rs12578698	0.84[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582616	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12810851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812783	1.00[AFR][1000 genomes]
rs12815393	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817365	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823653	1.00[CHB][hapmap]
rs12823699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828773	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830419	1.00[JPT][hapmap]
rs12831453	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560008	1.00[JPT][hapmap]
rs16913477	1.00[JPT][hapmap]
rs1861089	1.00[CHB][hapmap]
rs1863871	1.00[JPT][hapmap]
rs1990533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2080207	1.00[CHB][hapmap]
rs2114869	1.00[JPT][hapmap]
rs2114872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114873	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192433	0.84[ASN][1000 genomes]
rs2192434	0.84[ASN][1000 genomes]
rs2192435	0.84[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3176792	0.90[CEU][hapmap]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176806	1.00[JPT][hapmap]
rs34201389	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34850016	0.89[AFR][1000 genomes]
rs35237063	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763264	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763813	1.00[CHB][hapmap]
rs4763814	1.00[CHB][hapmap]
rs4763835	0.84[ASN][1000 genomes]
rs61913428	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6416258	1.00[JPT][hapmap]
rs6488065	1.00[JPT][hapmap]
rs6488109	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488122	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[JPT][hapmap]
rs7302110	1.00[JPT][hapmap]
rs7302746	1.00[JPT][hapmap]
rs7304321	1.00[JPT][hapmap]
rs7304464	1.00[JPT][hapmap]
rs7309800	1.00[JPT][hapmap]
rs7310568	1.00[JPT][hapmap]
rs7310790	1.00[JPT][hapmap]
rs7310897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311421	1.00[JPT][hapmap]
rs7311574	1.00[JPT][hapmap]
rs7311945	1.00[JPT][hapmap]
rs7312624	1.00[JPT][hapmap]
rs7485402	1.00[CHB][hapmap]
rs7954062	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961416	1.00[JPT][hapmap]
rs7961812	1.00[CHB][hapmap]
rs7962321	1.00[JPT][hapmap]
rs7969074	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7972035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap]
rs7975557	1.00[CHB][hapmap]
rs7978187	1.00[JPT][hapmap]
rs7979758	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929615	1.00[JPT][hapmap]
rs9630264	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668568	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs982511	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9919786	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12828602	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
4	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
5	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:9818000-9839800	Weak transcription	Ovary	ovary
8	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
9	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
10	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
12	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:9826800-9840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:9826800-9840600	Weak transcription	HSMMtube	muscle
16	chr12:9826800-9841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:9826800-9841400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
20	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
23	chr12:9827000-9840800	Weak transcription	Adipose Nuclei	Adipose
24	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:9827200-9838400	Weak transcription	Spleen	Spleen
26	chr12:9827200-9840200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:9827200-9840600	Weak transcription	HSMM	muscle
28	chr12:9827200-9841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:9827200-9847000	Weak transcription	NH-A	brain
30	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:9827200-9852400	Weak transcription	Osteobl	bone
35	chr12:9827400-9840600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:9827400-9849000	Weak transcription	A549	lung
37	chr12:9828800-9840600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:9832800-9846000	Weak transcription	Gastric	stomach
39	chr12:9833000-9839800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:9833000-9840600	Weak transcription	Dnd41	blood
41	chr12:9833000-9849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:9833200-9847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:9834000-9840800	Weak transcription	Placenta	Placenta
44	chr12:9834400-9840000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:9834400-9840600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:9835000-9840600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:9835200-9838200	Weak transcription	Lung	lung
48	chr12:9835400-9840200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:9835400-9849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:9835600-9839400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links