Variant report

Variant	rs2570265
Chromosome Location	chr15:52217344-52217345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1025184	0.85[CEU][hapmap]
rs1035737	0.85[CEU][hapmap]
rs11049	0.84[CEU][hapmap]
rs11070865	0.85[CEU][hapmap]
rs11070868	0.85[CEU][hapmap]
rs11630579	0.84[CEU][hapmap]
rs11630943	0.85[CEU][hapmap]
rs11637876	0.85[CEU][hapmap]
rs12593708	0.86[CEU][hapmap]
rs12905283	0.85[CEU][hapmap]
rs12908327	0.85[CEU][hapmap]
rs12915015	0.88[CEU][hapmap]
rs12915568	0.83[CEU][hapmap]
rs16953082	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964505	1.00[JPT][hapmap]
rs16964506	0.82[JPT][hapmap]
rs16964508	0.82[JPT][hapmap]
rs16964532	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964555	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964561	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964579	0.90[ASN][1000 genomes]
rs16964585	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964596	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964639	0.90[ASN][1000 genomes]
rs16964645	0.90[ASN][1000 genomes]
rs17526463	0.85[CEU][hapmap]
rs17526760	0.85[CEU][hapmap]
rs17611193	0.85[CEU][hapmap]
rs17611465	1.00[CHB][hapmap]
rs1840708	0.85[CEU][hapmap]
rs1863429	0.81[AMR][1000 genomes]
rs1863430	0.83[CEU][hapmap]
rs1972419	0.87[AMR][1000 genomes]
rs1991267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007335	0.83[CEU][hapmap]
rs2007355	0.82[CEU][hapmap]
rs2009972	0.89[CEU][hapmap]
rs2010026	0.83[CEU][hapmap]
rs2011995	0.83[CEU][hapmap]
rs2016057	1.00[CHB][hapmap]
rs2034856	0.85[CEU][hapmap]
rs2052705	0.82[CEU][hapmap]
rs2052706	0.84[CEU][hapmap]
rs2052708	0.83[CEU][hapmap]
rs2052709	0.83[CEU][hapmap]
rs2114191	0.85[CEU][hapmap]
rs2241503	0.82[CEU][hapmap]
rs2252606	0.82[CEU][hapmap]
rs2252831	0.88[CEU][hapmap]
rs2253116	0.85[CEU][hapmap]
rs2258248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433217	0.85[CEU][hapmap]
rs2433221	0.82[CEU][hapmap]
rs2436655	0.83[CEU][hapmap]
rs2436656	0.83[CEU][hapmap]
rs2436660	0.85[CEU][hapmap]
rs2441780	0.85[CEU][hapmap]
rs2448945	1.00[CHB][hapmap]
rs2448946	0.83[CEU][hapmap]
rs2448950	0.83[CEU][hapmap]
rs2448953	0.82[CEU][hapmap]
rs2470612	0.85[CEU][hapmap]
rs2554314	0.83[CEU][hapmap]
rs2554327	0.85[CEU][hapmap]
rs2554348	0.93[CEU][hapmap]
rs2554349	0.85[CEU][hapmap]
rs2554354	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs2570230	1.00[CHB][hapmap]
rs2570239	0.85[CEU][hapmap]
rs2570241	0.85[CEU][hapmap]
rs2570243	1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs2593169	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593170	0.85[CEU][hapmap]
rs2593173	0.85[CEU][hapmap]
rs2593181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593184	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593187	0.83[CEU][hapmap]
rs2593188	0.85[CEU][hapmap]
rs2593199	0.82[CEU][hapmap]
rs2593202	0.83[CEU][hapmap]
rs2622765	1.00[CHB][hapmap]
rs2623245	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs2623247	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs2623251	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs2623255	0.85[CEU][hapmap]
rs2623258	1.00[CHB][hapmap]
rs2623263	1.00[CHB][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs2623271	0.85[CEU][hapmap]
rs2623280	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2623281	0.83[CEU][hapmap]
rs2623282	0.83[CEU][hapmap]
rs2623283	0.86[CEU][hapmap]
rs2623291	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	1.00[CHB][hapmap]
rs2912186	0.83[CEU][hapmap]
rs2912187	0.85[CEU][hapmap]
rs2912189	0.85[CEU][hapmap]
rs2916169	0.83[CEU][hapmap]
rs2916172	0.85[CEU][hapmap]
rs2916176	0.85[CEU][hapmap]
rs2916177	0.85[CEU][hapmap]
rs2929423	0.83[CEU][hapmap]
rs2929424	0.83[CEU][hapmap]
rs2929425	0.85[CEU][hapmap]
rs2929426	0.85[CEU][hapmap]
rs2959285	0.89[CEU][hapmap]
rs2959293	0.82[CEU][hapmap]
rs2959296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959298	0.85[CEU][hapmap]
rs2959299	0.85[CEU][hapmap]
rs3751595	1.00[JPT][hapmap]
rs3794532	0.83[CEU][hapmap]
rs6493520	0.85[CEU][hapmap]
rs6493521	0.83[CEU][hapmap]
rs6493525	0.85[CEU][hapmap]
rs6493526	0.85[CEU][hapmap]
rs7162925	0.88[CEU][hapmap]
rs7163541	0.83[CEU][hapmap]
rs7165594	1.00[JPT][hapmap]
rs7170091	0.83[CEU][hapmap]
rs7171796	0.83[CEU][hapmap]
rs7174497	0.85[CEU][hapmap]
rs7174808	0.85[CEU][hapmap]
rs7178561	0.83[CEU][hapmap]
rs7178776	0.83[CEU][hapmap]
rs7179599	0.83[CEU][hapmap]
rs7181540	0.83[CEU][hapmap]
rs726158	0.83[CEU][hapmap]
rs8028922	0.85[CEU][hapmap]
rs8038344	0.83[CEU][hapmap]
rs9944235	0.83[CEU][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2570265	SCG3	cis	Temporal Cortex	GTEx
rs2570265	SCG3	cis	Brain Pons	GTEx
rs2570265	SCG3	cis	Cerebellum	GTEx
rs2570265	SCG3	cis	Frontal Cortex	GTEx
rs2570265	RP11-707P17.1	cis	Nerve Tibial	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	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:52180400-52218200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:52186400-52219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:52191000-52222800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
11	chr15:52194200-52228200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:52194200-52231600	Weak transcription	Psoas Muscle	Psoas
13	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
14	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:52196200-52234000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:52197000-52234200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:52198400-52219000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:52200400-52220800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
21	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:52201400-52217800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:52201800-52223000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:52202000-52230000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:52204400-52217800	Strong transcription	Fetal Intestine Small	intestine
26	chr15:52204600-52218400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:52204600-52224600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:52204800-52218800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:52204800-52219400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:52206600-52218400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr15:52207400-52219600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:52208000-52217400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:52208000-52217800	Strong transcription	Fetal Intestine Large	intestine
35	chr15:52208000-52218000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:52208000-52218200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:52208000-52218400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr15:52208000-52219000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:52208000-52222800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:52208200-52217800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:52208200-52217800	Strong transcription	Fetal Stomach	stomach
42	chr15:52208200-52218000	Strong transcription	Fetal Thymus	thymus
43	chr15:52208200-52218200	Strong transcription	Adipose Nuclei	Adipose
44	chr15:52208200-52218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:52208200-52219200	Strong transcription	Fetal Lung	lung
46	chr15:52208400-52218600	Strong transcription	Primary T cells from cord blood	blood
47	chr15:52208800-52218200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:52209000-52217800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:52209000-52218000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:52209000-52218600	Strong transcription	Placenta Amnion	Placenta Amnion

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