Variant report

Variant	rs6494997
Chromosome Location	chr15:72560642-72560643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72514333..72526693-chr15:72558323..72568559,52	MCF-7	breast:
2	chr15:72522943..72525408-chr15:72560443..72562421,3	MCF-7	breast:
3	chr15:72548498..72554612-chr15:72558312..72566000,13	MCF-7	breast:
4	chr15:72545613..72547175-chr15:72558549..72561473,2	MCF-7	breast:
5	chr15:72540888..72544821-chr15:72560401..72563677,4	MCF-7	breast:
6	chr15:72549309..72551782-chr15:72559287..72560861,2	MCF-7	breast:
7	chr15:72523582..72526035-chr15:72559818..72561426,2	K562	blood:
8	chr15:72558362..72561235-chr15:72766233..72767996,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261423	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1000281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1035744	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851850	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072349	0.90[EUR][1000 genomes]
rs11072350	0.91[EUR][1000 genomes]
rs11630170	0.89[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs11630611	0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs11633327	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634622	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442886	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12591338	0.83[CEU][hapmap]
rs12592044	0.82[TSI][hapmap]
rs12904652	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs13858	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs16956623	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16956634	0.83[CEU][hapmap]
rs2034879	0.94[MEX][hapmap];0.82[TSI][hapmap]
rs2052713	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278987	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2415134	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912231	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2957365	0.81[EUR][1000 genomes]
rs35603965	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759900	0.83[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3759902	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4506844	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55763892	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62022788	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022789	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494992	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs713048	0.89[CEU][hapmap]
rs7162299	0.94[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs7164780	0.81[EUR][1000 genomes]
rs7169264	0.83[EUR][1000 genomes]
rs7170456	0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7175197	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7175792	0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs7179427	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179942	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182776	0.82[TSI][hapmap]
rs7183055	0.82[EUR][1000 genomes]
rs7183196	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7183810	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023788	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs8025939	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs8027164	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs8027647	0.97[EUR][1000 genomes]
rs8030815	0.94[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs8032222	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037381	0.82[EUR][1000 genomes]
rs8038007	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8192362	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192386	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs8192431	0.83[CEU][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
4	nsv1601	chr15:72549885-72585176	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6494997	AAGAB	cis	cerebellum	SCAN
rs6494997	SENP8	cis	cerebellum	SCAN
rs6494997	PARP6	cis	parietal	SCAN
rs6494997	TIPIN	cis	parietal	SCAN
rs6494997	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72530400-72563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:72530800-72561200	Strong transcription	Adipose Nuclei	Adipose
3	chr15:72531000-72562400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:72531000-72563000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:72531000-72563000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:72531000-72563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:72531200-72562800	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:72531800-72561400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr15:72532000-72562600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:72532200-72561000	Strong transcription	Liver	Liver
11	chr15:72532200-72561000	Strong transcription	Fetal Intestine Large	intestine
12	chr15:72532200-72561600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:72532200-72562200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:72532200-72563000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:72532400-72562600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:72532600-72562200	Strong transcription	Brain Anterior Caudate	brain
17	chr15:72532600-72562800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:72532800-72563000	Strong transcription	HSMM	muscle
19	chr15:72533000-72562000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:72533200-72562400	Strong transcription	Hela-S3	cervix
21	chr15:72533200-72562600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr15:72536600-72564000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:72537200-72564200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:72537600-72563400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:72538600-72561200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:72538800-72562000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:72539000-72562200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:72539200-72562200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:72539400-72561200	Strong transcription	Left Ventricle	heart
30	chr15:72539400-72561600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:72539400-72562600	Strong transcription	Osteobl	bone
32	chr15:72539600-72561200	Strong transcription	Brain Germinal Matrix	brain
33	chr15:72539600-72562800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:72539800-72562800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:72540200-72561400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:72540200-72561600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:72540200-72561600	Strong transcription	HSMMtube	muscle
38	chr15:72540200-72562800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:72540200-72563200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:72540400-72561000	Strong transcription	Fetal Lung	lung
41	chr15:72540400-72561600	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr15:72540400-72562800	Strong transcription	A549	lung
43	chr15:72540400-72563400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:72540600-72560800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:72540600-72561000	Strong transcription	Lung	lung
46	chr15:72540600-72561400	Strong transcription	Placenta	Placenta
47	chr15:72540600-72561400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:72540600-72562000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:72540600-72562000	Strong transcription	Colon Smooth Muscle	Colon
50	chr15:72540600-72562200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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