Variant report

Variant	rs2623263
Chromosome Location	chr15:52182729-52182730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52182372..52184978-chr15:52197373..52199821,2	MCF-7	breast:
2	chr15:52180978..52184805-chr15:52187877..52189581,3	MCF-7	breast:
3	chr15:52120611..52123388-chr15:52180763..52183461,4	MCF-7	breast:
4	chr15:52181216..52183971-chr15:52196238..52198437,3	MCF-7	breast:
5	chr15:52164664..52167595-chr15:52181000..52183851,3	MCF-7	breast:
6	chr15:52178354..52182152-chr15:52182217..52184276,3	MCF-7	breast:
7	chr15:52174602..52177576-chr15:52179283..52182805,4	K562	blood:

Variant related genes	Relation type
ENSG00000272337	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000207484	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10444823	0.85[CEU][hapmap]
rs10775145	0.85[CEU][hapmap]
rs1133878	1.00[ASN][1000 genomes]
rs1133882	0.80[CEU][hapmap]
rs11630084	0.85[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]
rs1466276	0.81[CEU][hapmap]
rs1545602	0.85[CEU][hapmap]
rs16964482	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16964483	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1811326	0.85[CEU][hapmap]
rs1863429	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1867984	0.85[CEU][hapmap]
rs1902430	0.82[CEU][hapmap]
rs1972419	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972689	0.85[CEU][hapmap]
rs1991267	0.93[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2014638	0.85[CEU][hapmap]
rs2016057	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034857	0.85[CEU][hapmap]
rs2034858	0.85[CEU][hapmap]
rs2077743	0.85[CEU][hapmap]
rs2124587	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	0.86[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs2264339	0.85[CEU][hapmap]
rs2303443	0.85[CEU][hapmap]
rs2448810	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2554305	0.86[CEU][hapmap]
rs2554307	0.85[CEU][hapmap]
rs2554308	0.85[CEU][hapmap]
rs2554332	0.85[CEU][hapmap]
rs2554336	0.85[CEU][hapmap]
rs2554354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570224	0.85[CEU][hapmap]
rs2570228	0.85[CEU][hapmap]
rs2570230	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570233	0.85[CEU][hapmap]
rs2570243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570252	0.85[CEU][hapmap]
rs2570253	0.85[CEU][hapmap]
rs2570258	0.85[CEU][hapmap]
rs2570265	0.89[AMR][1000 genomes]
rs2593169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2593184	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2606130	1.00[ASN][1000 genomes]
rs2606133	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2622778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623245	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623254	0.85[CEU][hapmap]
rs2623258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623259	0.88[CEU][hapmap]
rs2623270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623280	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623291	0.89[AMR][1000 genomes]
rs2652595	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.82[AMR][1000 genomes]
rs28501427	1.00[ASN][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28718531	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs3751596	0.85[CEU][hapmap]
rs3794534	0.85[CEU][hapmap]
rs3794535	0.85[CEU][hapmap]
rs4238383	0.85[CEU][hapmap]
rs4622456	0.85[CEU][hapmap]
rs4774602	0.81[CEU][hapmap]
rs4775978	0.88[CEU][hapmap]
rs4775982	0.85[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	0.85[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]
rs8028258	0.85[CEU][hapmap]
rs8028890	0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2623263	SCG3	cis	cerebellum	SCAN
rs2623263	SCG3	cis	Cerebellum	GTEx
rs2623263	TRPM7	cis	parietal	SCAN
rs2623263	ONECUT1	cis	parietal	SCAN
rs2623263	SCG3	cis	Temporal Cortex	GTEx
rs2623263	SCG3	cis	Frontal Cortex	GTEx
rs2623263	SCG3	cis	Brain Pons	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52163000-52186800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:52163200-52184200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:52163400-52186200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:52165800-52183600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:52167200-52186200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:52167600-52192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:52167800-52188600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52168200-52183200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:52168600-52188600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:52168800-52183800	Weak transcription	Fetal Thymus	thymus
15	chr15:52170400-52186400	Weak transcription	Thymus	Thymus
16	chr15:52170400-52186600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:52170600-52184800	Weak transcription	Lung	lung
18	chr15:52170600-52186000	Weak transcription	Left Ventricle	heart
19	chr15:52171000-52184400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
21	chr15:52171200-52190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:52171600-52187000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:52171800-52183000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:52172200-52186000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:52172200-52186600	Weak transcription	Fetal Kidney	kidney
26	chr15:52172200-52190200	Weak transcription	Fetal Heart	heart
27	chr15:52172200-52192000	Weak transcription	Fetal Brain Male	brain
28	chr15:52172800-52208200	Weak transcription	Brain Angular Gyrus	brain
29	chr15:52173000-52184000	Weak transcription	Stomach Mucosa	stomach
30	chr15:52176400-52188600	Weak transcription	Small Intestine	intestine
31	chr15:52176600-52189000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:52177000-52184600	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:52177000-52188200	Weak transcription	Aorta	Aorta
34	chr15:52177000-52189800	Weak transcription	Colonic Mucosa	Colon
35	chr15:52177000-52192400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:52177000-52192400	Weak transcription	Gastric	stomach
37	chr15:52177000-52192400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:52177200-52184200	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:52177200-52188600	Weak transcription	Brain Anterior Caudate	brain
40	chr15:52177200-52192400	Weak transcription	Psoas Muscle	Psoas
41	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:52177400-52182800	Weak transcription	HMEC	breast
43	chr15:52177400-52183000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:52177400-52183600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:52177400-52186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:52177400-52186200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:52177400-52187600	Weak transcription	Ovary	ovary
48	chr15:52177400-52188600	Weak transcription	HSMMtube	muscle
49	chr15:52177400-52188600	Weak transcription	NHLF	lung
50	chr15:52177400-52190000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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