Variant report

Variant	rs2623247
Chromosome Location	chr15:52140231-52140232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52137753..52140319-chr15:52187826..52190548,2	MCF-7	breast:
2	chr15:52121713..52124493-chr15:52139618..52143592,4	MCF-7	breast:
3	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
4	chr15:52139835..52141814-chr15:52148000..52150770,2	MCF-7	breast:
5	chr15:52139382..52141080-chr15:52142666..52144648,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10444823	0.82[CEU][hapmap]
rs10775145	0.85[CEU][hapmap]
rs1133878	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1133882	0.81[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]
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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867984	0.83[CEU][hapmap]
rs1902430	0.82[CEU][hapmap]
rs1972419	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972689	0.85[CEU][hapmap]
rs1991267	1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes]
rs2014638	0.85[CEU][hapmap]
rs2016057	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034857	0.85[CEU][hapmap]
rs2034858	0.85[CEU][hapmap]
rs2077743	0.85[CEU][hapmap]
rs2124587	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs2264339	0.83[CEU][hapmap]
rs2303443	0.85[CEU][hapmap]
rs2448810	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
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];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570224	0.85[CEU][hapmap]
rs2570228	0.85[CEU][hapmap]
rs2570230	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570233	0.83[CEU][hapmap]
rs2570243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570252	0.83[CEU][hapmap]
rs2570253	0.83[CEU][hapmap]
rs2570258	0.85[CEU][hapmap]
rs2570265	0.87[AMR][1000 genomes]
rs2593169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2593184	0.94[AMR][1000 genomes]
rs2606128	0.81[AMR][1000 genomes]
rs2606130	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623245	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623254	0.83[CEU][hapmap]
rs2623258	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623259	0.88[CEU][hapmap]
rs2623263	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]
rs2623270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623291	0.87[AMR][1000 genomes]
rs2652595	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.84[AMR][1000 genomes]
rs28501427	1.00[ASN][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs3751596	0.85[CEU][hapmap]
rs3794534	0.83[CEU][hapmap]
rs3794535	0.85[CEU][hapmap]
rs4238383	0.85[CEU][hapmap]
rs4622456	0.83[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]
rs6493519	0.83[CEU][hapmap]
rs6493523	0.85[CEU][hapmap]
rs691738	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];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	0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2623247	SCG3	cis	Cerebellum	GTEx
rs2623247	SCG3	cis	Brain Pons	GTEx
rs2623247	SCG3	cis	Frontal Cortex	GTEx
rs2623247	SCG3	cis	Temporal Cortex	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:52133000-52143600	Enhancers	NHDF-Ad	bronchial
4	chr15:52133000-52146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:52134600-52142000	Enhancers	NHLF	lung
6	chr15:52135800-52146200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:52135800-52155000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:52136000-52145800	Weak transcription	Liver	Liver
9	chr15:52136000-52155200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:52136200-52155000	Weak transcription	Aorta	Aorta
11	chr15:52136600-52153400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:52137200-52140600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr15:52137200-52141600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:52137400-52147400	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:52137600-52141000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:52137600-52141400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:52137600-52145600	Weak transcription	HepG2	liver
18	chr15:52137800-52140400	Enhancers	Thymus	Thymus
19	chr15:52137800-52155000	Weak transcription	Fetal Intestine Large	intestine
20	chr15:52138000-52141200	Weak transcription	Pancreas	Pancrea
21	chr15:52138000-52153400	Weak transcription	Esophagus	oesophagus
22	chr15:52138000-52155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:52138600-52155000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:52139000-52141800	Enhancers	HUVEC	blood vessel
25	chr15:52139000-52146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:52139000-52153400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:52139200-52140400	Enhancers	HSMM	muscle
28	chr15:52139200-52141000	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:52139200-52141000	Weak transcription	Fetal Stomach	stomach
30	chr15:52139200-52141000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:52139200-52141000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:52139200-52141200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:52139200-52147600	Weak transcription	Brain Anterior Caudate	brain
34	chr15:52139200-52156200	Weak transcription	Fetal Intestine Small	intestine
35	chr15:52139400-52140800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:52139400-52141000	Weak transcription	Right Atrium	heart
37	chr15:52139400-52141200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:52139400-52141200	Weak transcription	Left Ventricle	heart
39	chr15:52139400-52141200	Weak transcription	Psoas Muscle	Psoas
40	chr15:52139400-52141800	Weak transcription	Right Ventricle	heart
41	chr15:52139400-52142400	Weak transcription	Spleen	Spleen
42	chr15:52139400-52142600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:52139400-52142800	Weak transcription	K562	blood
44	chr15:52139400-52143000	Weak transcription	Lung	lung
45	chr15:52139400-52144800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:52139400-52145000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:52139400-52145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:52139400-52147200	Weak transcription	GM12878-XiMat	blood
49	chr15:52139400-52147400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:52139400-52148200	Weak transcription	Duodenum Mucosa	Duodenum

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