Variant report

Variant	rs7176875
Chromosome Location	chr15:77832675-77832676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr15:77789053..77790918-chr15:77831495..77833590,2	MCF-7	breast:
4	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
5	chr15:77822048..77824496-chr15:77832446..77834927,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11630540	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630557	0.94[ASN][1000 genomes]
rs11630916	0.94[ASN][1000 genomes]
rs11630926	0.90[ASN][1000 genomes]
rs11631274	0.93[ASN][1000 genomes]
rs11634174	0.91[JPT][hapmap]
rs11635567	0.93[ASN][1000 genomes]
rs11635606	0.90[ASN][1000 genomes]
rs11636529	0.93[ASN][1000 genomes]
rs11639293	0.91[JPT][hapmap]
rs12898370	0.91[JPT][hapmap]
rs12898656	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12899390	0.93[ASN][1000 genomes]
rs12901100	0.92[ASN][1000 genomes]
rs12901471	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12901732	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12901765	0.93[ASN][1000 genomes]
rs12901998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12902072	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs12902379	0.91[ASN][1000 genomes]
rs12902698	0.89[JPT][hapmap]
rs12902896	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12902898	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs12902925	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904254	1.00[JPT][hapmap]
rs12904348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904584	0.93[ASN][1000 genomes]
rs12904709	0.93[ASN][1000 genomes]
rs12904823	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs12909292	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs12909645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12909808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910512	0.93[ASN][1000 genomes]
rs12910513	0.93[ASN][1000 genomes]
rs12910594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910951	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12910975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12911854	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12911963	0.81[JPT][hapmap]
rs12912386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12914098	0.96[ASN][1000 genomes]
rs12914932	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs12915548	0.93[ASN][1000 genomes]
rs12916515	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12916642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12916682	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12916822	0.93[ASN][1000 genomes]
rs12916833	0.93[ASN][1000 genomes]
rs12916973	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12917044	0.84[JPT][hapmap]
rs12917175	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12917314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17394732	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs34020536	0.90[ASN][1000 genomes]
rs34829483	0.97[ASN][1000 genomes]
rs35577135	0.96[ASN][1000 genomes]
rs59418918	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62009067	0.90[ASN][1000 genomes]
rs62009069	0.93[ASN][1000 genomes]
rs62009071	0.89[ASN][1000 genomes]
rs62009087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119	0.88[CEU][hapmap]
rs7176307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7180732	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7181283	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8025968	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs8032405	0.96[ASN][1000 genomes]
rs8033067	0.96[ASN][1000 genomes]
rs8033654	0.96[ASN][1000 genomes]
rs8040318	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs8040702	0.82[JPT][hapmap]
rs8041398	0.96[ASN][1000 genomes]
rs8041520	0.96[ASN][1000 genomes]
rs8042307	0.86[CHD][hapmap];0.82[JPT][hapmap]

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
rs7176875	HMG20A	cis	parietal	SCAN
rs7176875	HMG20A	cis	cerebellum	SCAN
rs7176875	STRA6	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
2	chr15:77827000-77833200	Weak transcription	HSMMtube	muscle
3	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
4	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
5	chr15:77827600-77834000	Enhancers	Primary B cells from peripheral blood	blood
6	chr15:77828400-77833400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:77828400-77835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:77828400-77835400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr15:77828400-77835400	Enhancers	Brain Anterior Caudate	brain
10	chr15:77828600-77833200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:77828600-77834000	Enhancers	Primary B cells from cord blood	blood
12	chr15:77828600-77834200	Enhancers	Brain Substantia Nigra	brain
13	chr15:77828800-77833400	Weak transcription	K562	blood
14	chr15:77829000-77833000	Weak transcription	Fetal Intestine Large	intestine
15	chr15:77829400-77835000	Enhancers	Fetal Muscle Trunk	muscle
16	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:77829600-77835400	Enhancers	Fetal Stomach	stomach
18	chr15:77829800-77835400	Enhancers	Fetal Brain Female	brain
19	chr15:77830000-77835200	Enhancers	Fetal Muscle Leg	muscle
20	chr15:77830200-77833000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:77830400-77833600	Weak transcription	Fetal Intestine Small	intestine
22	chr15:77830600-77832800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:77831200-77833400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:77831200-77835000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:77831400-77833200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:77831400-77833200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:77831400-77833600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:77831400-77833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:77831400-77833800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:77831400-77834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:77831400-77835200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:77831600-77833000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:77831600-77833000	Weak transcription	Fetal Brain Male	brain
34	chr15:77831600-77833000	Weak transcription	Fetal Heart	heart
35	chr15:77831600-77833400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:77831600-77835000	Enhancers	Spleen	Spleen
37	chr15:77831600-77835200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:77831800-77832800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:77831800-77832800	Weak transcription	Right Ventricle	heart
40	chr15:77831800-77832800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:77831800-77832800	Weak transcription	GM12878-XiMat	blood
42	chr15:77831800-77833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:77831800-77833200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:77831800-77833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:77831800-77833400	Weak transcription	Left Ventricle	heart
46	chr15:77831800-77833600	Weak transcription	Colonic Mucosa	Colon
47	chr15:77831800-77834200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:77831800-77835200	Weak transcription	Ovary	ovary
49	chr15:77832000-77833000	Weak transcription	Brain Angular Gyrus	brain
50	chr15:77832000-77833000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links