Variant report

Variant	rs2593169
Chromosome Location	chr15:52224522-52224523
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	CEBPB	chr15:52224519-52224751	HepG2	liver:	n/a	chr15:52224627-52224638
2	POLR2A	chr15:52223989-52224691	A549	lung:	n/a	n/a
3	CEBPB	chr15:52224494-52224723	A549	lung:	n/a	chr15:52224627-52224638

Variant related genes	Relation type
TMOD3	TF binding region
ENSG00000259556	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10444823	0.82[CEU][hapmap]
rs10775145	0.85[CEU][hapmap]
rs11630084	0.83[CEU][hapmap]
rs11636345	0.85[CEU][hapmap]
rs11638820	0.85[CEU][hapmap]
rs12903707	0.85[CEU][hapmap]
rs12917133	0.82[CEU][hapmap]
rs1350174	0.82[CEU][hapmap]
rs1545602	0.83[CEU][hapmap]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1811326	0.85[CEU][hapmap]
rs1863429	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1867984	0.83[CEU][hapmap]
rs1972419	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972689	0.85[CEU][hapmap]
rs1991267	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2014638	0.85[CEU][hapmap]
rs2016057	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2034857	0.85[CEU][hapmap]
rs2034858	0.85[CEU][hapmap]
rs2077743	0.85[CEU][hapmap]
rs2124587	1.00[ASN][1000 genomes]
rs2258248	1.00[CHB][hapmap];0.92[AMR][1000 genomes]
rs2264339	0.83[CEU][hapmap]
rs2303443	0.85[CEU][hapmap]
rs2448810	1.00[ASN][1000 genomes]
rs2448945	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2554305	0.83[CEU][hapmap]
rs2554307	0.83[CEU][hapmap]
rs2554308	0.83[CEU][hapmap]
rs2554332	0.83[CEU][hapmap]
rs2554336	0.85[CEU][hapmap]
rs2554354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs2570224	0.85[CEU][hapmap]
rs2570228	0.85[CEU][hapmap]
rs2570230	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2570233	0.83[CEU][hapmap]
rs2570243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570252	0.83[CEU][hapmap]
rs2570253	0.83[CEU][hapmap]
rs2570258	0.85[CEU][hapmap]
rs2570265	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593181	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593184	0.92[AMR][1000 genomes]
rs2606130	1.00[ASN][1000 genomes]
rs2606133	1.00[ASN][1000 genomes]
rs2606147	1.00[ASN][1000 genomes]
rs2622765	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623245	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623254	0.83[CEU][hapmap]
rs2623258	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623259	0.88[CEU][hapmap]
rs2623263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623280	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2623291	0.94[AMR][1000 genomes]
rs2652595	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28501427	1.00[ASN][1000 genomes]
rs28718531	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs3751596	0.85[CEU][hapmap]
rs3794534	0.83[CEU][hapmap]
rs3794535	0.85[CEU][hapmap]
rs4238383	0.85[CEU][hapmap]
rs4774602	0.81[CEU][hapmap]
rs4775978	0.85[CEU][hapmap]
rs4775982	0.83[CEU][hapmap]
rs4775983	0.85[CEU][hapmap]
rs55922236	1.00[ASN][1000 genomes]
rs56049741	1.00[ASN][1000 genomes]
rs56186119	1.00[ASN][1000 genomes]
rs62015208	1.00[ASN][1000 genomes]
rs6493519	0.83[CEU][hapmap]
rs6493523	0.85[CEU][hapmap]
rs691738	1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]
rs7165283	0.85[CEU][hapmap]
rs7165585	0.85[CEU][hapmap]
rs7181553	0.85[CEU][hapmap]
rs8024265	1.00[ASN][1000 genomes]
rs8028890	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2593169	SCG3	cis	Brain Pons	GTEx
rs2593169	SCG3	cis	Temporal Cortex	GTEx
rs2593169	SCG3	cis	Frontal Cortex	GTEx
rs2593169	SCG3	cis	Cerebellum	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
5	chr15:52194200-52228200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:52194200-52231600	Weak transcription	Psoas Muscle	Psoas
7	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
8	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52196200-52234000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:52197000-52234200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
13	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:52202000-52230000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:52204600-52224600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:52210000-52233600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:52211200-52230400	Weak transcription	K562	blood
20	chr15:52211600-52228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
23	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
24	chr15:52214000-52226200	Weak transcription	Ovary	ovary
25	chr15:52215200-52234000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:52215800-52226200	Weak transcription	Fetal Brain Female	brain
27	chr15:52216000-52229600	Weak transcription	Colonic Mucosa	Colon
28	chr15:52216000-52238600	Weak transcription	Pancreas	Pancrea
29	chr15:52216200-52227400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:52216400-52229600	Weak transcription	HSMMtube	muscle
31	chr15:52216400-52234200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:52217000-52227200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:52217000-52231600	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:52217200-52226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52217200-52227600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:52217200-52227800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:52217200-52228400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:52217200-52231600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:52217200-52238400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:52217200-52238800	Weak transcription	Brain Angular Gyrus	brain
41	chr15:52217600-52234200	Weak transcription	NHLF	lung
42	chr15:52217600-52238800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:52217800-52227800	Weak transcription	Fetal Intestine Large	intestine
44	chr15:52217800-52228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:52217800-52228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:52217800-52228600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:52217800-52237400	Weak transcription	Aorta	Aorta
48	chr15:52217800-52237400	Weak transcription	Brain Anterior Caudate	brain
49	chr15:52217800-52239000	Weak transcription	Gastric	stomach
50	chr15:52218000-52226000	Weak transcription	Spleen	Spleen

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