Variant report

Variant	rs4777590
Chromosome Location	chr15:73407088-73407089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73404038..73406058-chr15:73406406..73408423,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1023924	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1038137	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10438294	0.94[CHD][hapmap]
rs10467948	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10467949	0.86[CHD][hapmap]
rs11072403	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632639	0.83[JPT][hapmap]
rs12050774	0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12899246	0.83[JPT][hapmap]
rs12902768	0.81[CHB][hapmap]
rs13379875	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1479337	0.82[JPT][hapmap]
rs1479338	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1479339	0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1479340	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs1564345	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap]
rs17762146	0.89[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs17762600	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs17829830	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs17829957	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1871385	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs1964543	0.87[EUR][1000 genomes]
rs2046017	0.86[CHD][hapmap]
rs2127277	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap]
rs2169951	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251205	0.86[CHD][hapmap]
rs2415147	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2415148	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2899784	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3736510	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs3743489	0.87[CHB][hapmap]
rs3784793	0.92[CHB][hapmap]
rs3985588	0.82[ASN][1000 genomes]
rs4132535	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4132536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4375637	0.87[CHB][hapmap]
rs4545783	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4609810	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4776624	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4776625	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4777582	0.83[JPT][hapmap]
rs4777589	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4777591	0.83[JPT][hapmap]
rs55646651	0.80[ASN][1000 genomes]
rs55836604	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55925663	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56269104	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377702	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59066156	0.81[ASN][1000 genomes]
rs62016797	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016803	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016805	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016806	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62016808	0.87[EUR][1000 genomes]
rs62016809	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62016811	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016813	0.87[EUR][1000 genomes]
rs62016814	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62016849	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62016851	0.84[ASN][1000 genomes]
rs62016853	0.82[ASN][1000 genomes]
rs62017774	0.81[ASN][1000 genomes]
rs6495047	0.81[JPT][hapmap]
rs7164894	0.83[JPT][hapmap]
rs7165610	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169083	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7172021	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap]
rs7172396	0.80[CHB][hapmap]
rs7175329	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs74025262	0.82[ASN][1000 genomes]
rs747872	0.81[CHB][hapmap]
rs747873	0.80[CHB][hapmap];1.00[CHD][hapmap]
rs8026121	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026579	0.87[JPT][hapmap]
rs8042700	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs922516	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs9920186	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs9972347	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4777590	GRAMD2	cis	parietal	SCAN
rs4777590	THAP10	cis	cerebellum	SCAN
rs4777590	MYO9A	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73384600-73409200	Weak transcription	Fetal Lung	lung
2	chr15:73388800-73431200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:73393200-73422400	Weak transcription	Aorta	Aorta
4	chr15:73394200-73414800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:73394400-73415000	Weak transcription	Fetal Stomach	stomach
6	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
7	chr15:73397200-73409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:73398400-73415000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:73400400-73434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:73401200-73409200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:73401200-73414600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:73401200-73414800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:73401200-73423000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:73401200-73428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:73401400-73408800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:73401400-73408800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:73401400-73409000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:73401400-73410600	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:73401400-73413000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:73401400-73419600	Weak transcription	Brain Angular Gyrus	brain
21	chr15:73401400-73422400	Weak transcription	Pancreas	Pancrea
22	chr15:73401400-73422800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
24	chr15:73401600-73413600	Weak transcription	Brain Substantia Nigra	brain
25	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
26	chr15:73403200-73414800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:73403600-73414800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:73403600-73415600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:73404200-73409000	Weak transcription	Ovary	ovary
30	chr15:73404200-73414800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:73404200-73425800	Weak transcription	Small Intestine	intestine
32	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
33	chr15:73404800-73409200	Weak transcription	Fetal Intestine Small	intestine
34	chr15:73405800-73415000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:73406600-73408600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:73406600-73410400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:73406600-73410400	Weak transcription	Fetal Intestine Large	intestine
38	chr15:73406600-73422400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:73406600-73423200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:73406600-73425200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:73406600-73432600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:73406800-73414800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:73406800-73418600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:73406800-73419600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:73407000-73414800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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