Variant report

Variant	rs2470617
Chromosome Location	chr15:52266878-52266879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52266394..52269371-chr17:57935595..57937194,2	MCF-7	breast:
2	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
3	chr15:52264304..52267297-chr15:52410135..52412517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1025184	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap]
rs1035737	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs10775145	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs11049	0.96[CEU][hapmap]
rs11630579	0.96[CEU][hapmap]
rs11637876	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12593708	0.96[CEU][hapmap]
rs12903707	0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs12905283	0.96[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs12908327	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12915015	0.96[CEU][hapmap]
rs12915568	0.96[CEU][hapmap]
rs17526463	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs17526760	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs17611193	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs17705732	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs1811326	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs1863430	0.96[CEU][hapmap]
rs1867984	0.85[CHB][hapmap]
rs1972689	0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs1991267	0.82[CEU][hapmap]
rs2007335	0.96[CEU][hapmap]
rs2007355	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2009972	0.85[CEU][hapmap]
rs2011995	0.96[CEU][hapmap]
rs2014638	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs2052705	0.96[CEU][hapmap]
rs2052706	0.96[CEU][hapmap]
rs2052708	0.96[CEU][hapmap]
rs2052709	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap]
rs2114191	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs2241503	0.89[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs2252606	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs2252831	1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs2253116	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs2258248	0.82[CEU][hapmap]
rs2264339	0.84[CHB][hapmap]
rs2303443	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2414122	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs2433217	0.96[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2433221	0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs2436655	0.96[CEU][hapmap]
rs2436656	0.95[CEU][hapmap]
rs2436660	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2441780	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2448946	0.96[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2448950	0.96[CEU][hapmap]
rs2448953	0.96[CEU][hapmap]
rs2470612	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs2554305	0.84[CHB][hapmap]
rs2554307	0.84[CHB][hapmap]
rs2554308	0.85[CHB][hapmap]
rs2554314	0.96[CEU][hapmap]
rs2554315	0.86[CHD][hapmap]
rs2554327	0.96[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs2554336	0.89[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2554348	0.86[CEU][hapmap]
rs2554349	0.89[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap]
rs2570224	0.82[ASW][hapmap];0.83[GIH][hapmap];0.84[TSI][hapmap]
rs2570228	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs2570233	0.85[CHB][hapmap]
rs2570239	0.96[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs2570241	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2570258	0.81[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2593170	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs2593173	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap]
rs2593185	0.89[CHB][hapmap]
rs2593187	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs2593188	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap]
rs2593199	0.96[CEU][hapmap]
rs2593202	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[YRI][hapmap]
rs2623254	0.84[CHB][hapmap]
rs2623255	0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap]
rs2623271	0.96[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs2623281	0.96[CEU][hapmap];0.84[CHB][hapmap]
rs2623282	0.96[CEU][hapmap]
rs2623283	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs2912186	0.96[CEU][hapmap]
rs2912187	0.96[CEU][hapmap]
rs2912189	0.96[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs2916169	0.96[CEU][hapmap]
rs2916172	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2916176	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2916177	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2929423	0.96[CEU][hapmap]
rs2929424	0.96[CEU][hapmap]
rs2929425	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2929426	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2959285	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2959293	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs2959298	0.96[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap]
rs2959299	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs3751596	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs3794532	0.96[CEU][hapmap]
rs3794534	0.81[CHB][hapmap]
rs3794535	0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs4775982	0.84[CHB][hapmap]
rs4775983	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs6493520	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs6493521	0.96[CEU][hapmap]
rs6493523	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs6493525	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs6493526	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs7162925	0.96[CEU][hapmap]
rs7163541	0.96[CEU][hapmap]
rs7165283	0.81[CHB][hapmap]
rs7170091	0.96[CEU][hapmap]
rs7171796	0.96[CEU][hapmap]
rs7178561	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs7178776	0.96[CEU][hapmap]
rs7179599	0.96[CEU][hapmap]
rs8028922	0.96[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs8038344	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
6	esv15501	chr15:52265256-52273371	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
7	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv442376	chr15:52265735-52273284	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
9	nsv514781	chr15:52265740-52273308	Strong transcription Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
10	nsv569411	chr15:52266878-52270680	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
11	nsv569412	chr15:52266878-52272701	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
12	nsv569413	chr15:52266878-52273132	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
13	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2470617	SCG3	cis	Frontal Cortex	GTEx
rs2470617	SCG3	cis	Cerebellum	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52264600-52273000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:52264600-52273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:52264600-52273000	Weak transcription	Liver	Liver
4	chr15:52264600-52273000	Weak transcription	Right Ventricle	heart
5	chr15:52264600-52273600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:52264600-52273600	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:52264600-52273600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:52264600-52273600	Weak transcription	Stomach Mucosa	stomach
9	chr15:52264600-52273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:52264600-52273800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:52264600-52273800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:52264600-52273800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:52264600-52273800	Weak transcription	Brain Substantia Nigra	brain
14	chr15:52264600-52273800	Weak transcription	Thymus	Thymus
15	chr15:52264600-52274000	Weak transcription	Colonic Mucosa	Colon
16	chr15:52264600-52274200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:52264600-52274400	Weak transcription	Pancreas	Pancrea
18	chr15:52264800-52269600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:52264800-52273000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:52264800-52273000	Weak transcription	Hela-S3	cervix
21	chr15:52264800-52273200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:52264800-52273200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:52264800-52273600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:52264800-52273600	Weak transcription	NHEK	skin
25	chr15:52264800-52273800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:52264800-52273800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:52264800-52273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:52264800-52273800	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:52264800-52274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:52264800-52274000	Weak transcription	Fetal Intestine Large	intestine
31	chr15:52265000-52267200	Weak transcription	Fetal Stomach	stomach
32	chr15:52265000-52273000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:52265000-52273800	Weak transcription	HSMM	muscle
34	chr15:52265200-52267200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:52265200-52269800	Weak transcription	Fetal Brain Female	brain
36	chr15:52265200-52273000	Weak transcription	Fetal Thymus	thymus
37	chr15:52265200-52273800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:52265200-52273800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:52265400-52273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52265600-52273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:52265800-52267000	Strong transcription	Fetal Intestine Small	intestine
42	chr15:52265800-52272600	Weak transcription	HepG2	liver
43	chr15:52266000-52267000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:52266400-52273800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:52266600-52269800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:52266600-52273800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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