Variant report

Variant	rs11630540
Chromosome Location	chr15:77833625-77833626
allele	A/G
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	chr15:77795830..77799057-chr15:77830706..77834217,3	MCF-7	breast:
2	chr15:77777712..77780447-chr15:77832272..77835232,2	MCF-7	breast:
3	chr15:77828874..77831053-chr15:77833422..77835199,2	MCF-7	breast:
4	chr15:77824813..77828626-chr15:77832957..77835709,3	K562	blood:
5	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
6	chr15:77833246..77835948-chr15:77846373..77848114,2	MCF-7	breast:
7	chr15:77412894..77414915-chr15:77833378..77835255,2	K562	blood:
8	chr15:77822048..77824496-chr15:77832446..77834927,2	K562	blood:

No data

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11630557	0.93[ASN][1000 genomes]
rs11630916	0.93[ASN][1000 genomes]
rs11630926	0.89[ASN][1000 genomes]
rs11631274	0.91[ASN][1000 genomes]
rs11634174	0.83[JPT][hapmap]
rs11635567	0.91[ASN][1000 genomes]
rs11635606	0.89[ASN][1000 genomes]
rs11636529	0.91[ASN][1000 genomes]
rs11639293	0.83[JPT][hapmap]
rs12898370	0.83[JPT][hapmap]
rs12899390	0.91[ASN][1000 genomes]
rs12901100	0.90[ASN][1000 genomes]
rs12901471	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12901732	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12901765	0.91[ASN][1000 genomes]
rs12901998	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902072	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs12902379	0.89[ASN][1000 genomes]
rs12902898	0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12902925	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904212	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904254	0.86[JPT][hapmap]
rs12904348	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904584	0.91[ASN][1000 genomes]
rs12904709	0.91[ASN][1000 genomes]
rs12904823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12909292	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12909645	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12909808	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12910512	0.91[ASN][1000 genomes]
rs12910513	0.91[ASN][1000 genomes]
rs12910594	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12910951	0.82[CHB][hapmap]
rs12910975	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12911854	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12912386	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12914098	0.94[ASN][1000 genomes]
rs12914932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12915548	0.91[ASN][1000 genomes]
rs12916515	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916642	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916822	0.91[ASN][1000 genomes]
rs12916833	0.91[ASN][1000 genomes]
rs12917044	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12917175	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12917314	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs17394732	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34020536	0.89[ASN][1000 genomes]
rs34829483	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35577135	0.97[ASN][1000 genomes]
rs59418918	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009067	0.89[ASN][1000 genomes]
rs62009069	0.91[ASN][1000 genomes]
rs62009071	0.87[ASN][1000 genomes]
rs62009087	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119	0.84[CEU][hapmap]
rs7176307	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176875	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180732	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7181283	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs8025968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8032405	0.94[ASN][1000 genomes]
rs8033067	0.94[ASN][1000 genomes]
rs8033654	0.94[ASN][1000 genomes]
rs8041398	0.97[ASN][1000 genomes]
rs8041520	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11630540	HMG20A	cis	parietal	SCAN
rs11630540	STRA6	cis	cerebellum	SCAN
rs11630540	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
2	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
3	chr15:77827600-77834000	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:77828400-77835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:77828400-77835400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:77828400-77835400	Enhancers	Brain Anterior Caudate	brain
7	chr15:77828600-77834000	Enhancers	Primary B cells from cord blood	blood
8	chr15:77828600-77834200	Enhancers	Brain Substantia Nigra	brain
9	chr15:77829400-77835000	Enhancers	Fetal Muscle Trunk	muscle
10	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:77829600-77835400	Enhancers	Fetal Stomach	stomach
12	chr15:77829800-77835400	Enhancers	Fetal Brain Female	brain
13	chr15:77830000-77835200	Enhancers	Fetal Muscle Leg	muscle
14	chr15:77831200-77835000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:77831400-77833800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:77831400-77834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:77831400-77835200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr15:77831600-77835000	Enhancers	Spleen	Spleen
19	chr15:77831600-77835200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:77831800-77834200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:77831800-77835200	Weak transcription	Ovary	ovary
22	chr15:77832000-77834200	Weak transcription	Osteobl	bone
23	chr15:77832000-77835000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:77832000-77835400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:77832200-77834800	Weak transcription	Gastric	stomach
26	chr15:77832200-77835200	Weak transcription	Fetal Thymus	thymus
27	chr15:77832400-77835000	Weak transcription	Pancreas	Pancrea
28	chr15:77832600-77835200	Enhancers	Brain Germinal Matrix	brain
29	chr15:77832600-77835400	Enhancers	Brain Cingulate Gyrus	brain
30	chr15:77832600-77835400	Enhancers	Placenta	Placenta
31	chr15:77832800-77834000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:77832800-77834200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:77832800-77835000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr15:77832800-77835400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:77832800-77835400	Enhancers	Right Ventricle	heart
36	chr15:77832800-77836000	Enhancers	NHDF-Ad	bronchial
37	chr15:77833000-77833800	Enhancers	Fetal Heart	heart
38	chr15:77833000-77833800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr15:77833000-77834000	Enhancers	Fetal Intestine Large	intestine
40	chr15:77833000-77834200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr15:77833000-77834200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:77833000-77834600	Enhancers	Fetal Lung	lung
43	chr15:77833000-77835000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:77833000-77835000	Weak transcription	Lung	lung
45	chr15:77833000-77835200	Enhancers	Brain Angular Gyrus	brain
46	chr15:77833000-77835200	Enhancers	Brain Hippocampus Middle	brain
47	chr15:77833000-77835600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr15:77833000-77836600	Enhancers	Fetal Brain Male	brain
49	chr15:77833200-77833800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr15:77833200-77834000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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