Variant report

Variant	rs16964482
Chromosome Location	chr15:52008565-52008566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52008451..52011571-chr15:52027342..52031770,5	MCF-7	breast:
2	chr15:52007487..52009839-chr15:52012657..52014790,2	MCF-7	breast:
3	chr15:51965377..51967473-chr15:52008396..52010538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1133878	1.00[ASN][1000 genomes]
rs16964483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1972419	1.00[ASN][1000 genomes]
rs1991267	1.00[CHB][hapmap]
rs2016057	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2124587	1.00[ASN][1000 genomes]
rs2448810	1.00[ASN][1000 genomes]
rs2448945	1.00[CHB][hapmap]
rs2554354	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2554355	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2554358	1.00[ASN][1000 genomes]
rs2570230	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2570243	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap]
rs2606130	1.00[ASN][1000 genomes]
rs2606133	1.00[ASN][1000 genomes]
rs2606147	1.00[ASN][1000 genomes]
rs2622765	1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs2622778	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623245	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623247	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623251	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623258	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623263	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623270	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2652595	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28522862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28876142	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691738	1.00[ASN][1000 genomes]

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	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16964482	SCG3	cis	Frontal Cortex	GTEx
rs16964482	SCG3	cis	Temporal Cortex	GTEx
rs16964482	SCG3	cis	Cerebellum	GTEx
rs16964482	SCG3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
4	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:51995400-52013200	Weak transcription	Brain Substantia Nigra	brain
11	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
12	chr15:52000000-52013800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:52000800-52024000	Weak transcription	Gastric	stomach
14	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
15	chr15:52001200-52013000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:52001600-52012000	Weak transcription	Primary B cells from cord blood	blood
17	chr15:52002400-52013600	Strong transcription	Fetal Brain Female	brain
18	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:52003400-52013200	Weak transcription	Aorta	Aorta
20	chr15:52004000-52013400	Strong transcription	Brain Germinal Matrix	brain
21	chr15:52004400-52009800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:52004400-52016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:52004800-52012600	Weak transcription	Primary T cells from cord blood	blood
24	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
25	chr15:52005200-52009000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:52006200-52013000	Weak transcription	Esophagus	oesophagus
27	chr15:52006400-52013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:52006600-52012000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:52006800-52013400	Weak transcription	K562	blood
31	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
32	chr15:52007400-52009000	Strong transcription	Brain Angular Gyrus	brain
33	chr15:52007400-52009200	Enhancers	Fetal Intestine Small	intestine
34	chr15:52007400-52013000	Weak transcription	Dnd41	blood
35	chr15:52007400-52013400	Enhancers	Fetal Intestine Large	intestine
36	chr15:52007600-52013400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:52007600-52016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:52007800-52010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:52007800-52016800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
41	chr15:52008000-52013400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:52008400-52008800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain

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