Variant report

Variant	rs2959296
Chromosome Location	chr15:52259870-52259871
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52258228..52260672-chr15:52262065..52264472,4	K562	blood:
2	chr15:52259391..52261500-chr15:52261701..52265538,4	MCF-7	breast:
3	chr15:52258924..52260672-chr15:52262065..52263877,2	K562	blood:
4	chr15:52253083..52256570-chr15:52257033..52260699,4	MCF-7	breast:
5	chr15:52257155..52261897-chr15:52262401..52265766,14	MCF-7	breast:
6	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069956	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1025184	0.84[CEU][hapmap]
rs1035737	0.84[CEU][hapmap]
rs11049	0.82[CEU][hapmap]
rs11630579	0.82[CEU][hapmap]
rs11637876	0.84[CEU][hapmap]
rs12593708	0.84[CEU][hapmap]
rs12905283	0.84[CEU][hapmap]
rs12908327	0.84[CEU][hapmap]
rs12915015	0.86[CEU][hapmap]
rs12915568	0.81[CEU][hapmap]
rs16953082	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
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	0.84[CEU][hapmap]
rs17526760	0.84[CEU][hapmap]
rs17611193	0.84[CEU][hapmap]
rs17611465	1.00[CHB][hapmap]
rs1863430	0.81[CEU][hapmap]
rs1972419	0.83[AMR][1000 genomes]
rs1991267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007335	0.81[CEU][hapmap]
rs2007355	0.80[CEU][hapmap]
rs2009972	0.92[CEU][hapmap]
rs2010026	0.81[CEU][hapmap]
rs2011995	0.81[CEU][hapmap]
rs2016057	1.00[CHB][hapmap]
rs2034856	0.84[CEU][hapmap]
rs2052705	0.80[CEU][hapmap]
rs2052706	0.82[CEU][hapmap]
rs2052708	0.81[CEU][hapmap]
rs2052709	0.81[CEU][hapmap]
rs2114191	0.84[CEU][hapmap]
rs2241503	0.84[CEU][hapmap]
rs2252831	0.86[CEU][hapmap]
rs2253116	0.84[CEU][hapmap]
rs2258248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433217	0.84[CEU][hapmap]
rs2433221	0.80[CEU][hapmap]
rs2436655	0.81[CEU][hapmap]
rs2436656	0.80[CEU][hapmap]
rs2436660	0.84[CEU][hapmap]
rs2441780	0.84[CEU][hapmap]
rs2448945	1.00[CHB][hapmap]
rs2448946	0.81[CEU][hapmap]
rs2448950	0.81[CEU][hapmap]
rs2448953	0.80[CEU][hapmap]
rs2470612	0.83[CEU][hapmap]
rs2554314	0.81[CEU][hapmap]
rs2554327	0.84[CEU][hapmap]
rs2554348	0.92[CEU][hapmap]
rs2554349	0.84[CEU][hapmap]
rs2554354	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs2570230	1.00[CHB][hapmap]
rs2570239	0.84[CEU][hapmap]
rs2570241	0.84[CEU][hapmap]
rs2570243	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2570265	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs2593170	0.84[CEU][hapmap]
rs2593173	0.84[CEU][hapmap]
rs2593181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593184	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593187	0.81[CEU][hapmap]
rs2593188	0.84[CEU][hapmap]
rs2593199	0.80[CEU][hapmap]
rs2593202	0.81[CEU][hapmap]
rs2623245	1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs2623247	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2623251	1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs2623255	0.84[CEU][hapmap]
rs2623258	1.00[CHB][hapmap]
rs2623263	1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2623271	0.84[CEU][hapmap]
rs2623280	0.90[AMR][1000 genomes]
rs2623281	0.81[CEU][hapmap]
rs2623282	0.81[CEU][hapmap]
rs2623283	0.84[CEU][hapmap]
rs2623291	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912186	0.81[CEU][hapmap]
rs2912187	0.84[CEU][hapmap]
rs2912189	0.84[CEU][hapmap]
rs2916169	0.81[CEU][hapmap]
rs2916172	0.84[CEU][hapmap]
rs2916176	0.84[CEU][hapmap]
rs2916177	0.84[CEU][hapmap]
rs2929423	0.81[CEU][hapmap]
rs2929424	0.81[CEU][hapmap]
rs2929425	0.84[CEU][hapmap]
rs2929426	0.84[CEU][hapmap]
rs2959285	0.87[CEU][hapmap]
rs2959293	0.80[CEU][hapmap]
rs2959298	0.84[CEU][hapmap]
rs2959299	0.84[CEU][hapmap]
rs3794532	0.81[CEU][hapmap]
rs6493520	0.84[CEU][hapmap]
rs6493521	0.81[CEU][hapmap]
rs6493525	0.84[CEU][hapmap]
rs6493526	0.84[CEU][hapmap]
rs7162925	0.87[CEU][hapmap]
rs7163541	0.81[CEU][hapmap]
rs7170091	0.81[CEU][hapmap]
rs7171796	0.81[CEU][hapmap]
rs7178561	0.81[CEU][hapmap]
rs7178776	0.81[CEU][hapmap]
rs7179599	0.81[CEU][hapmap]
rs726158	0.81[CEU][hapmap]
rs8028922	0.84[CEU][hapmap]
rs8038344	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv569410	chr15:52257874-52273132	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2959296	SCG3	cis	Cerebellum	GTEx
rs2959296	SCG3	cis	Frontal Cortex	GTEx
rs2959296	SCG3	cis	Brain Pons	GTEx
rs2959296	SCG3	cis	Temporal Cortex	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52244600-52262600	Weak transcription	Fetal Heart	heart
3	chr15:52245600-52261800	Weak transcription	Pancreas	Pancrea
4	chr15:52245600-52262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:52245800-52263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:52245800-52263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52246400-52262200	Weak transcription	NHLF	lung
8	chr15:52247000-52262400	Weak transcription	Colonic Mucosa	Colon
9	chr15:52249800-52263000	Weak transcription	Psoas Muscle	Psoas
10	chr15:52253200-52262400	Weak transcription	Fetal Brain Male	brain
11	chr15:52253200-52262800	Weak transcription	HSMMtube	muscle
12	chr15:52253200-52263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:52253400-52262400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52253400-52262400	Weak transcription	Esophagus	oesophagus
15	chr15:52253600-52263000	Weak transcription	Right Ventricle	heart
16	chr15:52253800-52261800	Weak transcription	Small Intestine	intestine
17	chr15:52253800-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:52253800-52263200	Weak transcription	Gastric	stomach
19	chr15:52254200-52261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52254200-52262200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:52254200-52262400	Weak transcription	Spleen	Spleen
22	chr15:52254200-52262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:52254200-52262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52254200-52263200	Weak transcription	Left Ventricle	heart
25	chr15:52254400-52260000	Weak transcription	Lung	lung
26	chr15:52254400-52261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:52254400-52262400	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:52254400-52263000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:52254400-52263200	Weak transcription	Ovary	ovary
30	chr15:52254600-52261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:52254600-52262800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:52255000-52262000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:52255000-52262000	Weak transcription	K562	blood
34	chr15:52255000-52262200	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:52255000-52262200	Weak transcription	HMEC	breast
36	chr15:52255000-52262400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:52255000-52262400	Weak transcription	HSMM	muscle
38	chr15:52255200-52262000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:52255600-52262400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:52256600-52261200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:52257800-52263000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr15:52258000-52260000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr15:52258000-52260400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:52258000-52261200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:52258000-52262000	Weak transcription	NHDF-Ad	bronchial
46	chr15:52258000-52262200	Weak transcription	Osteobl	bone
47	chr15:52258200-52262600	Weak transcription	NH-A	brain
48	chr15:52258400-52261800	Weak transcription	Liver	Liver
49	chr15:52258400-52262200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:52258400-52262200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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