Variant report

Variant	rs1971272
Chromosome Location	chr10:18939676-18939677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18939570..18941733-chr6:27856904..27858914,2	MCF-7	breast:
2	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
3	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165997	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000152487	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1055114	0.84[EUR][1000 genomes]
rs10764566	1.00[JPT][hapmap]
rs10764584	1.00[JPT][hapmap]
rs10828835	1.00[JPT][hapmap]
rs10828859	1.00[JPT][hapmap]
rs10828879	1.00[JPT][hapmap]
rs10828906	1.00[JPT][hapmap]
rs11015307	1.00[JPT][hapmap]
rs11015416	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11015454	1.00[ASN][1000 genomes]
rs12772534	1.00[JPT][hapmap]
rs1352655	1.00[JPT][hapmap]
rs17621077	0.83[CEU][hapmap];0.88[TSI][hapmap]
rs17622920	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17623007	1.00[ASN][1000 genomes]
rs17693687	0.88[CEU][hapmap]
rs17695669	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2035752	1.00[ASN][1000 genomes]
rs34503140	1.00[ASN][1000 genomes]
rs4279920	1.00[ASN][1000 genomes]
rs45499092	0.85[EUR][1000 genomes]
rs45580334	1.00[ASN][1000 genomes]
rs45615535	0.82[EUR][1000 genomes]
rs4578284	1.00[JPT][hapmap]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4748480	1.00[JPT][hapmap]
rs4748495	1.00[JPT][hapmap]
rs58225473	0.80[EUR][1000 genomes]
rs58857018	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59643191	0.89[EUR][1000 genomes]
rs61298471	1.00[ASN][1000 genomes]
rs6482516	1.00[JPT][hapmap]
rs6482529	1.00[JPT][hapmap]
rs7070044	0.83[EUR][1000 genomes]
rs7073651	1.00[JPT][hapmap]
rs7073751	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081811	1.00[JPT][hapmap]
rs7088214	1.00[JPT][hapmap]
rs7093518	1.00[ASN][1000 genomes]
rs7095070	1.00[JPT][hapmap]
rs7098313	1.00[JPT][hapmap]
rs7099975	1.00[JPT][hapmap]
rs7902450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7905432	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7905730	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7917217	1.00[ASN][1000 genomes]
rs7917323	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1971272	ARL5B	cis	cerebellum	SCAN
rs1971272	CACNB2	cis	cerebellum	SCAN
rs1971272	NSUN6	cis	parietal	SCAN
rs1971272	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs1971272	NSUN6	cis	lung	GTEx
rs1971272	NSUN6	cis	Artery Aorta	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
2	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
3	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:18917000-18940200	Weak transcription	Lung	lung
6	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
7	chr10:18937000-18941400	Active TSS	GM12878-XiMat	blood
8	chr10:18937600-18941400	Active TSS	K562	blood
9	chr10:18937800-18940800	Active TSS	Liver	Liver
10	chr10:18937800-18941000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:18938200-18939800	Active TSS	Brain Angular Gyrus	brain
12	chr10:18938200-18940000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr10:18938200-18941200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr10:18938200-18941400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:18938400-18939800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:18938400-18941200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr10:18938400-18941200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr10:18938400-18941200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr10:18938400-18941200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr10:18938600-18940000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:18938600-18941200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr10:18938600-18941200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:18938600-18941200	Active TSS	Ovary	ovary
24	chr10:18938600-18941400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:18938600-18941400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:18938800-18940000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr10:18938800-18940200	Active TSS	Fetal Brain Male	brain
28	chr10:18938800-18940800	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr10:18938800-18941200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:18938800-18941200	Active TSS	Fetal Intestine Large	intestine
31	chr10:18938800-18941200	Active TSS	NHLF	lung
32	chr10:18939000-18939800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:18939000-18939800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr10:18939000-18939800	Flanking Active TSS	NHDF-Ad	bronchial
35	chr10:18939000-18940000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:18939000-18940000	Flanking Active TSS	HUVEC	blood vessel
37	chr10:18939000-18940200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr10:18939000-18940200	Active TSS	Brain Germinal Matrix	brain
39	chr10:18939000-18940800	Active TSS	Hela-S3	cervix
40	chr10:18939000-18941000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:18939000-18941000	Active TSS	HepG2	liver
42	chr10:18939000-18941200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr10:18939000-18941200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:18939000-18941200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr10:18939000-18941200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:18939000-18941200	Active TSS	Right Ventricle	heart
47	chr10:18939200-18939800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr10:18939200-18939800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr10:18939200-18939800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr10:18939200-18939800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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