Variant report

Variant	rs2094196
Chromosome Location	chr13:48513557-48513558
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	CTCF	chr13:48513420-48513570	HAc	cerebellar:	n/a	n/a
2	CTCF	chr13:48513440-48513590	NB4	blood:	n/a	n/a
3	CTCF	chr13:48513420-48513570	AG09309	skin:	n/a	n/a
4	CTCF	chr13:48513440-48513590	HBMEC	blood vessel:	n/a	n/a
5	CTCF	chr13:48513420-48513570	HFF-Myc	foreskin:	n/a	n/a

Variant related genes	Relation type
SUCLA2	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10397	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1104351	1.00[JPT][hapmap]
rs11617143	1.00[CHB][hapmap]
rs12874522	1.00[JPT][hapmap]
rs13243	0.90[ASN][1000 genomes]
rs1326137	1.00[JPT][hapmap]
rs1886977	1.00[JPT][hapmap]
rs2094190	1.00[JPT][hapmap]
rs2406694	1.00[JPT][hapmap]
rs4331249	0.81[ASN][1000 genomes]
rs4941618	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4941624	1.00[JPT][hapmap]
rs4942719	0.82[EUR][1000 genomes]
rs4942720	1.00[JPT][hapmap]
rs4942721	1.00[JPT][hapmap]
rs56385117	0.90[ASN][1000 genomes]
rs6561414	1.00[JPT][hapmap]
rs7323702	1.00[JPT][hapmap]
rs7323821	1.00[JPT][hapmap]
rs7324919	0.90[ASN][1000 genomes]
rs7325175	1.00[JPT][hapmap]
rs7326861	1.00[CHB][hapmap]
rs7329137	1.00[JPT][hapmap]
rs7329266	1.00[JPT][hapmap]
rs7329615	1.00[JPT][hapmap]
rs7331746	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7332363	1.00[JPT][hapmap]
rs7332994	1.00[JPT][hapmap]
rs7335662	1.00[CHB][hapmap]
rs7335797	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7335869	0.81[ASN][1000 genomes]
rs7337521	1.00[CHB][hapmap]
rs7339238	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs753372	1.00[JPT][hapmap]
rs7981492	1.00[CHB][hapmap]
rs7981902	1.00[CHB][hapmap]
rs7989765	0.81[ASN][1000 genomes]
rs7990099	1.00[JPT][hapmap]
rs7991892	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7993196	0.81[ASN][1000 genomes]
rs7996051	1.00[JPT][hapmap]
rs7996581	1.00[JPT][hapmap]
rs7999270	1.00[JPT][hapmap]
rs8001032	1.00[JPT][hapmap]
rs8002322	0.81[MEX][hapmap]
rs8002482	1.00[JPT][hapmap]
rs840429	1.00[JPT][hapmap]
rs840432	1.00[JPT][hapmap]
rs840439	1.00[JPT][hapmap]
rs943067	1.00[JPT][hapmap]
rs9526419	1.00[JPT][hapmap]
rs9526455	1.00[JPT][hapmap]
rs9534872	0.81[ASN][1000 genomes]
rs9534884	1.00[JPT][hapmap]
rs9534934	1.00[JPT][hapmap]
rs9534966	1.00[JPT][hapmap]
rs9562772	0.81[ASN][1000 genomes]
rs9562780	0.81[ASN][1000 genomes]
rs9562781	0.81[ASN][1000 genomes]
rs9562784	0.90[ASN][1000 genomes]
rs9562785	1.00[CHB][hapmap]
rs9562791	1.00[CHB][hapmap]
rs9567927	1.00[JPT][hapmap]
rs9567944	0.81[ASN][1000 genomes]
rs9567945	0.81[ASN][1000 genomes]
rs9567946	0.81[ASN][1000 genomes]
rs9567956	0.90[ASN][1000 genomes]
rs9567971	1.00[CHB][hapmap]
rs9567975	1.00[CHB][hapmap]
rs9567977	1.00[CHB][hapmap]
rs9567978	1.00[CHB][hapmap]
rs9567982	1.00[CHB][hapmap]
rs9567988	1.00[JPT][hapmap]
rs9567990	1.00[CHB][hapmap]
rs9567992	1.00[CHB][hapmap]
rs9634811	0.81[ASN][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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2094196	SUCLA2	cis	cerebellum	SCAN
rs2094196	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs2094196	MED4	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
2	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48502600-48513600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:48503800-48516800	Weak transcription	NHDF-Ad	bronchial
5	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
7	chr13:48507200-48524000	Weak transcription	Lung	lung
8	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
9	chr13:48507800-48513600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:48507800-48513600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr13:48507800-48515200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr13:48507800-48515200	Weak transcription	Osteobl	bone
13	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
14	chr13:48508000-48514000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr13:48508000-48514200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:48508000-48514200	Weak transcription	Fetal Stomach	stomach
17	chr13:48508000-48515200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:48508000-48515200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:48508000-48515400	Weak transcription	Fetal Kidney	kidney
20	chr13:48508000-48516200	Weak transcription	Brain Substantia Nigra	brain
21	chr13:48508000-48522400	Weak transcription	GM12878-XiMat	blood
22	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:48508200-48515400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:48508200-48515800	Weak transcription	Psoas Muscle	Psoas
25	chr13:48508200-48520000	Weak transcription	HepG2	liver
26	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr13:48508400-48513600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr13:48508400-48513600	Weak transcription	HMEC	breast
29	chr13:48508400-48515200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr13:48508600-48513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:48508600-48515400	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:48508600-48530800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:48508800-48514200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:48508800-48515200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr13:48508800-48522000	Weak transcription	NH-A	brain
36	chr13:48509000-48513800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:48509000-48515200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr13:48509000-48530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr13:48509200-48514000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr13:48509200-48514200	Weak transcription	HSMMtube	muscle
41	chr13:48509200-48528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:48509400-48513600	Weak transcription	Primary B cells from cord blood	blood
43	chr13:48509400-48515200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:48510200-48513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:48510200-48515400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr13:48510600-48514000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:48510600-48514000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr13:48510600-48515400	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:48510800-48517400	Strong transcription	Primary T cells from cord blood	blood
50	chr13:48510800-48517400	Strong transcription	Left Ventricle	heart

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