Variant report

Variant	rs869301
Chromosome Location	chr15:77830633-77830634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77828874..77831053-chr15:77833422..77835199,2	MCF-7	breast:
2	chr15:77829651..77831982-chr15:77834371..77837022,2	MCF-7	breast:
3	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1005752	0.95[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1022172	0.85[EUR][1000 genomes]
rs11072653	0.81[JPT][hapmap]
rs11633054	0.86[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs11854328	0.84[JPT][hapmap]
rs11857450	0.81[ASW][hapmap];0.95[CEU][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11857860	0.81[ASW][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs1191196	0.81[JPT][hapmap]
rs12324627	0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12900004	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs12901130	0.94[JPT][hapmap]
rs12901503	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12907746	0.86[JPT][hapmap]
rs12910361	0.83[EUR][1000 genomes]
rs1473922	0.81[JPT][hapmap]
rs1565756	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2055901	0.86[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs34591043	0.86[CEU][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs4886866	0.81[JPT][hapmap]
rs4886869	0.91[JPT][hapmap]
rs4886875	0.81[ASW][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap]
rs4886876	0.90[JPT][hapmap]
rs4886877	0.82[ASW][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs59153558	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62009090	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6495240	0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs7170877	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7171448	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7172144	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177055	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7178572	0.86[CEU][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs8024485	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs8034133	0.85[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs907388	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952471	0.81[EUR][1000 genomes]
rs952472	0.83[EUR][1000 genomes]
rs965480	0.80[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs869301	MPI	cis	cerebellum	SCAN
rs869301	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77819800-77831000	Weak transcription	Gastric	stomach
2	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
3	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
4	chr15:77825800-77831000	Weak transcription	Stomach Mucosa	stomach
5	chr15:77827000-77833200	Weak transcription	HSMMtube	muscle
6	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
7	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
8	chr15:77827600-77832400	Enhancers	Pancreas	Pancrea
9	chr15:77827600-77834000	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:77827800-77831200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:77828400-77831400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr15:77828400-77831800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:77828400-77831800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:77828400-77832000	Enhancers	Brain Hippocampus Middle	brain
15	chr15:77828400-77832400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:77828400-77833400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:77828400-77835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:77828400-77835400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:77828400-77835400	Enhancers	Brain Anterior Caudate	brain
20	chr15:77828600-77831200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr15:77828600-77831400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr15:77828600-77831600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr15:77828600-77831600	Enhancers	Brain Germinal Matrix	brain
24	chr15:77828600-77831800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr15:77828600-77832000	Enhancers	Brain Angular Gyrus	brain
26	chr15:77828600-77832000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:77828600-77833200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:77828600-77834000	Enhancers	Primary B cells from cord blood	blood
29	chr15:77828600-77834200	Enhancers	Brain Substantia Nigra	brain
30	chr15:77828800-77831400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:77828800-77831600	Weak transcription	Placenta	Placenta
32	chr15:77828800-77832200	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:77828800-77833400	Weak transcription	K562	blood
34	chr15:77829000-77831200	Weak transcription	Fetal Heart	heart
35	chr15:77829000-77831200	Enhancers	Spleen	Spleen
36	chr15:77829000-77831800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:77829000-77833000	Weak transcription	Fetal Intestine Large	intestine
38	chr15:77829200-77830800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:77829400-77831200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:77829400-77831400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:77829400-77831400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:77829400-77835000	Enhancers	Fetal Muscle Trunk	muscle
43	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:77829600-77831600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr15:77829600-77835400	Enhancers	Fetal Stomach	stomach
46	chr15:77829800-77831000	Enhancers	Fetal Brain Male	brain
47	chr15:77829800-77831000	Flanking Active TSS	GM12878-XiMat	blood
48	chr15:77829800-77835400	Enhancers	Fetal Brain Female	brain
49	chr15:77830000-77831400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr15:77830000-77832000	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links