Variant report

Variant	rs6488109
Chromosome Location	chr12:9825969-9825970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:9825946-9826772	K562	blood:	n/a	n/a
2	POLR2A	chr12:9825672-9827322	GM18951	blood:	n/a	n/a
3	POLR2A	chr12:9825909-9827311	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:9822858-9827605	GM12891	blood:	n/a	n/a
5	MTA3	chr12:9825386-9827372	GM12878	blood:	n/a	n/a
6	PAX5	chr12:9825948-9826784	GM12878	blood:	n/a	n/a
7	TEAD4	chr12:9825933-9826691	K562	blood:	n/a	n/a
8	POLR2A	chr12:9825775-9827205	GM12892	blood:	n/a	n/a
9	TEAD4	chr12:9825964-9826749	K562	blood:	n/a	n/a
10	POLR2A	chr12:9825908-9826867	K562	blood:	n/a	n/a
11	POLR2A	chr12:9825851-9827196	GM19193	blood:	n/a	n/a
12	POLR2A	chr12:9823968-9827308	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:9825691-9827317	GM18526	blood:	n/a	n/a
14	TCF7L2	chr12:9825869-9826217	MCF-7	breast:	n/a	n/a
15	POLR2A	chr12:9822835-9827266	GM12892	blood:	n/a	n/a
16	POLR2A	chr12:9824036-9827274	GM12878	blood:	n/a	n/a
17	RUNX3	chr12:9825904-9827225	GM12878	blood:	n/a	n/a
18	RELA	chr12:9825916-9827190	GM19193	blood:	n/a	n/a
19	RELA	chr12:9825751-9827270	GM18951	blood:	n/a	n/a
20	TBL1XR1	chr12:9825850-9826691	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:9825418-9827310	GM19099	blood:	n/a	n/a
22	JUN	chr12:9825463-9827142	K562	blood:	n/a	n/a
23	TCF12	chr12:9825960-9826897	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr12:9821389-9827321	Raji	blood:	n/a	n/a
25	RELA	chr12:9825668-9827181	GM12891	blood:	n/a	n/a
26	ZNF384	chr12:9825922-9826259	K562	blood:	n/a	n/a
27	STAT5A	chr12:9825867-9827121	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:9825925-9827149	GM12878	blood:	n/a	n/a
29	NFIC	chr12:9825788-9826914	SK-N-SH	brain:	n/a	n/a
30	ATF2	chr12:9825890-9827287	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:9822941-9827304	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:9822886-9827320	GM12878	blood:	n/a	n/a
33	CHD1	chr12:9825943-9826650	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:9825447-9826721	GM12878	blood:	n/a	n/a
35	RELA	chr12:9825638-9827244	GM19099	blood:	n/a	n/a
36	EBF1	chr12:9825866-9826232	GM12878	blood:	n/a	n/a
37	NFIC	chr12:9825909-9826932	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:

No data

Variant related genes	Relation type
CLEC2D	TF binding region
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10844418	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844424	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844449	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844457	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844476	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052303	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052304	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052305	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052311	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052327	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052342	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052366	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052367	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052430	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052431	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052434	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052718	0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs11519377	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11524523	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309762	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320830	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12582616	0.83[ASN][1000 genomes]
rs12810851	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12815393	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817365	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12825507	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828602	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828773	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831453	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2114872	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114873	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.83[ASN][1000 genomes]
rs35237063	1.00[ASN][1000 genomes]
rs4763264	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.83[ASN][1000 genomes]
rs6488122	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7310897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954062	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962025	0.90[AFR][1000 genomes]
rs7969074	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972035	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979758	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630264	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630265	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9668568	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982511	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6488109	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
3	chr12:9807000-9826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
6	chr12:9813000-9826200	Weak transcription	Gastric	stomach
7	chr12:9813800-9826000	Weak transcription	NHDF-Ad	bronchial
8	chr12:9815000-9826000	Weak transcription	Lung	lung
9	chr12:9815000-9826000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:9815000-9826200	Weak transcription	Colonic Mucosa	Colon
11	chr12:9815000-9826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:9815000-9826400	Weak transcription	Fetal Intestine Small	intestine
13	chr12:9815200-9826200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:9815200-9828400	Weak transcription	Liver	Liver
15	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
16	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
17	chr12:9815600-9826000	Weak transcription	Spleen	Spleen
18	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:9817000-9826000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
23	chr12:9817600-9826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:9818000-9826000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:9818000-9826000	Weak transcription	Fetal Stomach	stomach
26	chr12:9818000-9826000	Weak transcription	Left Ventricle	heart
27	chr12:9818000-9826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:9818000-9839800	Weak transcription	Ovary	ovary
30	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
31	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
32	chr12:9818200-9826200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:9818200-9826400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:9818200-9828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:9818600-9826000	Weak transcription	Adipose Nuclei	Adipose
37	chr12:9818600-9826000	Weak transcription	Fetal Lung	lung
38	chr12:9819200-9826000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:9821400-9826000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:9822200-9826000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr12:9822400-9827200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:9823000-9829800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
43	chr12:9823600-9826600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:9823800-9826000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:9823800-9826000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:9824200-9826000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:9824200-9827400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:9824200-9827800	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr12:9824200-9828200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
50	chr12:9824200-9828200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links