Variant report

Variant	rs2570243
Chromosome Location	chr15:52138967-52138968
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	chr15:52137753..52140319-chr15:52187826..52190548,2	MCF-7	breast:
3	chr15:52120473..52124016-chr15:52133834..52139102,7	K562	blood:
4	chr15:52120690..52123150-chr15:52137386..52139102,2	K562	blood:
5	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
6	chr15:52129040..52133421-chr15:52134334..52139621,6	K562	blood:
7	chr15:52121037..52122634-chr15:52137236..52139208,2	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	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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867984	0.83[CEU][hapmap]
rs1902430	0.82[CEU][hapmap]
rs1972419	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972689	0.85[CEU][hapmap]
rs1991267	1.00[CHB][hapmap];0.89[AMR][1000 genomes]
rs2014638	0.85[CEU][hapmap]
rs2016057	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[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	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	1.00[CHB][hapmap]
rs2264339	0.83[CEU][hapmap]
rs2303443	0.85[CEU][hapmap]
rs2448810	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.88[CEU][hapmap];0.89[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];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570233	0.83[CEU][hapmap]
rs2570252	0.83[CEU][hapmap]
rs2570253	0.83[CEU][hapmap]
rs2570258	0.85[CEU][hapmap]
rs2570265	0.85[AMR][1000 genomes]
rs2593169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs2593184	0.92[AMR][1000 genomes]
rs2606128	0.83[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];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623259	0.88[CEU][hapmap]
rs2623263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623280	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623291	0.85[AMR][1000 genomes]
rs2652595	0.81[CEU][hapmap];1.00[CHB][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]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap];0.81[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[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
rs2570243	SCG3	cis	Temporal Cortex	GTEx
rs2570243	SCG3	cis	Frontal Cortex	GTEx
rs2570243	SCG3	cis	Cerebellum	GTEx
rs2570243	SCG3	cis	Brain Pons	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52123600-52140000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr15:52129000-52140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:52129200-52139800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr15:52129400-52140000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:52132200-52140200	Enhancers	Primary T cells from cord blood	blood
8	chr15:52132400-52139400	Enhancers	Stomach Mucosa	stomach
9	chr15:52133000-52143600	Enhancers	NHDF-Ad	bronchial
10	chr15:52133000-52146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:52133200-52139600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:52133200-52139800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:52133600-52139400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:52133600-52139600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:52133600-52140000	Enhancers	HMEC	breast
16	chr15:52134600-52139200	Enhancers	Colon Smooth Muscle	Colon
17	chr15:52134600-52139400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr15:52134600-52142000	Enhancers	NHLF	lung
19	chr15:52135000-52139400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr15:52135600-52140200	Weak transcription	Ovary	ovary
21	chr15:52135800-52139000	Weak transcription	Fetal Thymus	thymus
22	chr15:52135800-52139200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:52135800-52139400	Enhancers	K562	blood
24	chr15:52135800-52146200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:52135800-52155000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:52136000-52145800	Weak transcription	Liver	Liver
27	chr15:52136000-52155200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52136200-52155000	Weak transcription	Aorta	Aorta
29	chr15:52136600-52153400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:52137000-52139600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:52137000-52139600	Enhancers	Fetal Lung	lung
32	chr15:52137200-52139000	Enhancers	HSMM	muscle
33	chr15:52137200-52139200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr15:52137200-52139400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:52137200-52139400	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:52137200-52139400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:52137200-52139400	Enhancers	Fetal Heart	heart
38	chr15:52137200-52139400	Enhancers	Left Ventricle	heart
39	chr15:52137200-52139800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:52137200-52140000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:52137200-52140600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:52137200-52141600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr15:52137400-52139000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:52137400-52139200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr15:52137400-52139400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:52137400-52139400	Enhancers	Right Atrium	heart
47	chr15:52137400-52139400	Enhancers	Spleen	Spleen
48	chr15:52137400-52139600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr15:52137400-52139600	Enhancers	Dnd41	blood
50	chr15:52137400-52139600	Flanking Active TSS	Hela-S3	cervix

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