Variant report

Variant	rs10747608
Chromosome Location	chr12:51616582-51616583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:51616149-51616851	A549	lung:	n/a	n/a
2	SP1	chr12:51616097-51616756	A549	lung:	n/a	n/a
3	FOSL2	chr12:51616137-51616740	A549	lung:	n/a	n/a
4	BCL3	chr12:51616165-51616764	A549	lung:	n/a	n/a
5	SP1	chr12:51616058-51616846	A549	lung:	n/a	n/a
6	MAX	chr12:51616195-51616718	MCF-7	breast:	n/a	n/a
7	MAX	chr12:51616151-51616678	A549	lung:	n/a	n/a
8	FOXA2	chr12:51616207-51616934	A549	lung:	n/a	n/a
9	GATA3	chr12:51616233-51616669	T-47D	breast:	n/a	n/a
10	REST	chr12:51616208-51616749	A549	lung:	n/a	chr12:51616615-51616623
11	MAX	chr12:51616099-51616784	A549	lung:	n/a	n/a
12	POLR2A	chr12:51616581-51616782	GM12878	blood:	n/a	n/a
13	TCF12	chr12:51616075-51616907	A549	lung:	n/a	n/a
14	BCL3	chr12:51616126-51616627	A549	lung:	n/a	n/a
15	EP300	chr12:51616158-51616827	A549	lung:	n/a	n/a
16	EP300	chr12:51616168-51616836	A549	lung:	n/a	n/a
17	FOXA2	chr12:51616195-51616995	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51615081..51618060-chr12:51626400..51629742,3	MCF-7	breast:
2	chr12:51611630..51613404-chr12:51614974..51616606,2	K562	blood:
3	chr12:51615094..51616659-chr12:51630849..51632957,2	K562	blood:
4	chr12:51616235..51618059-chr12:51618373..51620555,2	K562	blood:
5	chr12:51610491..51614628-chr12:51614796..51620409,6	K562	blood:
6	chr12:51609133..51616659-chr12:51628963..51635200,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269339	TF binding region
ENSG00000183283	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000269339	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10735833	0.80[GIH][hapmap]
rs10783424	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs7311832	0.80[GIH][hapmap]
rs7398442	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7399018	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7399073	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953955	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10747608	ELA1	cis	multi-tissue	Pritchard
rs10747608	SPATS2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51612800-51619800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51612800-51621000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:51612800-51622200	Weak transcription	Lung	lung
4	chr12:51612800-51622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:51613000-51619000	Weak transcription	Fetal Brain Female	brain
6	chr12:51613000-51619200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:51613000-51619200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:51613000-51621200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:51613000-51621200	Weak transcription	Fetal Stomach	stomach
10	chr12:51613000-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:51613200-51618600	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:51613400-51617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:51613400-51621600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:51613400-51622400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:51613400-51631600	Weak transcription	Thymus	Thymus
16	chr12:51613400-51631800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:51613400-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:51613400-51632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:51613600-51620000	Weak transcription	Fetal Intestine Small	intestine
20	chr12:51613600-51631800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:51613600-51631800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:51613600-51631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:51613800-51618600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:51613800-51619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:51613800-51623600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:51614000-51618000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:51614200-51618600	Weak transcription	Fetal Brain Male	brain
28	chr12:51614200-51622200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:51614200-51631600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:51616000-51616800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:51616200-51616600	Enhancers	Liver	Liver
32	chr12:51616200-51616600	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr12:51616200-51616600	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:51616200-51616600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:51616200-51616600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr12:51616200-51616600	Flanking Active TSS	A549	lung
37	chr12:51616200-51616600	Enhancers	K562	blood
38	chr12:51616200-51616800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:51616200-51616800	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr12:51616200-51616800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:51616200-51616800	Enhancers	Fetal Lung	lung
42	chr12:51616200-51616800	Enhancers	HUVEC	blood vessel
43	chr12:51616400-51616600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr12:51616400-51616800	Flanking Active TSS	Ovary	ovary
45	chr12:51616400-51619000	Weak transcription	Brain Substantia Nigra	brain
46	chr12:51616400-51631600	Weak transcription	Gastric	stomach

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