Variant report

Variant	rs2623251
Chromosome Location	chr15:52133914-52133915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52131004..52134205-chr15:52136724..52139101,4	K562	blood:
2	chr15:52131973..52134112-chr20:52194712..52196799,2	MCF-7	breast:
3	chr15:52120473..52124016-chr15:52133834..52139102,7	K562	blood:
4	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
5	chr15:52132092..52134106-chr15:52134200..52135846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10444823	0.85[CEU][hapmap]
rs10775145	0.85[CEU][hapmap]
rs1133878	0.82[AMR][1000 genomes];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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867984	0.85[CEU][hapmap]
rs1902430	0.82[CEU][hapmap]
rs1972419	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[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];0.87[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	0.86[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs2264339	0.85[CEU][hapmap]
rs2303443	0.85[CEU][hapmap]
rs2448810	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[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];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.87[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	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570233	0.85[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	0.85[CEU][hapmap]
rs2570253	0.85[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];0.95[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	0.81[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	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	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	0.85[CEU][hapmap]
rs2623258	0.81[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[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]
rs2623270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[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	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][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];0.85[YRI][hapmap];0.83[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]
rs6493519	0.85[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	0.85[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
rs2623251	TRPM7	cis	parietal	SCAN
rs2623251	ONECUT1	cis	parietal	SCAN
rs2623251	SCG3	cis	Frontal Cortex	GTEx
rs2623251	SCG3	cis	Temporal Cortex	GTEx
rs2623251	SCG3	cis	Cerebellum	GTEx
rs2623251	SCG3	cis	cerebellum	SCAN
rs2623251	SCG3	cis	Brain Pons	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52123000-52134000	Weak transcription	Pancreas	Pancrea
2	chr15:52123600-52140000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr15:52124200-52134600	Weak transcription	HSMM	muscle
4	chr15:52124200-52134800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:52124200-52135000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:52124200-52135000	Weak transcription	Aorta	Aorta
7	chr15:52124200-52135400	Weak transcription	Thymus	Thymus
8	chr15:52125000-52137600	Weak transcription	Lung	lung
9	chr15:52129000-52136000	Enhancers	Fetal Lung	lung
10	chr15:52129000-52136600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr15:52129000-52140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:52129200-52139800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr15:52129400-52140000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:52130200-52134400	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:52130200-52134600	Weak transcription	Psoas Muscle	Psoas
17	chr15:52130200-52135000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:52130400-52134400	Weak transcription	NH-A	brain
19	chr15:52130400-52134600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:52130400-52134600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:52130400-52134600	Weak transcription	HSMMtube	muscle
22	chr15:52130400-52134800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:52130400-52134800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:52130400-52134800	Weak transcription	Osteobl	bone
25	chr15:52130400-52135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:52130400-52135000	Weak transcription	Brain Substantia Nigra	brain
27	chr15:52130400-52135200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:52130400-52137000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:52130400-52137600	Weak transcription	Placenta	Placenta
30	chr15:52130600-52134800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:52130600-52134800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:52130600-52134800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:52130600-52135000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:52130600-52135600	Weak transcription	Brain Anterior Caudate	brain
35	chr15:52130600-52136200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr15:52130800-52134000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:52130800-52134200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:52130800-52134200	Weak transcription	Fetal Heart	heart
39	chr15:52130800-52134400	Weak transcription	Liver	Liver
40	chr15:52130800-52134400	Weak transcription	Left Ventricle	heart
41	chr15:52130800-52134600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:52130800-52134600	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:52130800-52134600	Weak transcription	NHLF	lung
44	chr15:52130800-52135000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:52130800-52135200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:52130800-52136400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:52130800-52137400	Weak transcription	Esophagus	oesophagus
48	chr15:52130800-52137600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:52131000-52134400	Weak transcription	Ovary	ovary

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