Variant report

Variant	rs1919553
Chromosome Location	chr3:121440886-121440887
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	chr3:121422713..121424587-chr3:121439673..121442209,2	MCF-7	breast:
2	chr3:121439769..121441731-chr3:121445734..121447295,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10511407	1.00[CHB][hapmap]
rs10934556	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934557	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934561	1.00[CHB][hapmap]
rs11915822	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919421	1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486456	1.00[CHB][hapmap]
rs12488717	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489110	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489686	1.00[CHB][hapmap]
rs12491109	1.00[CHB][hapmap]
rs12491671	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491714	0.86[EUR][1000 genomes]
rs12492214	1.00[CHB][hapmap]
rs12492861	1.00[CHB][hapmap]
rs12493927	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636562	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12637265	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574654	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814668	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919554	0.84[JPT][hapmap];0.99[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1919556	1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971281	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2055034	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35674179	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825165	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805125	1.00[CHB][hapmap]
rs3805129	1.00[CHB][hapmap]
rs3966063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4048693	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271407	0.87[EUR][1000 genomes]
rs4610269	1.00[CHB][hapmap]
rs55930520	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964762	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109033	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56286202	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762575	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766737	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775634	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786605	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793556	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798575	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625960	1.00[CHB][hapmap]
rs7643293	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1919553	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:121418800-121442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:121426200-121442600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:121426200-121443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:121429000-121450000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr3:121429400-121442800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:121429400-121448800	Strong transcription	Primary hematopoietic stem cells	blood
10	chr3:121429400-121449000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:121430200-121442400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:121430200-121450000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:121430400-121441400	Strong transcription	Osteobl	bone
14	chr3:121430600-121449000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:121430600-121449400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:121430600-121450000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:121430800-121443600	Strong transcription	Placenta	Placenta
18	chr3:121430800-121448200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:121430800-121448800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:121430800-121448800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:121430800-121450000	Strong transcription	Fetal Intestine Large	intestine
22	chr3:121431000-121441000	Strong transcription	HepG2	liver
23	chr3:121431000-121442400	Strong transcription	GM12878-XiMat	blood
24	chr3:121431000-121444800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:121431000-121448600	Strong transcription	Adipose Nuclei	Adipose
26	chr3:121431000-121449000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:121431000-121449000	Strong transcription	Fetal Thymus	thymus
28	chr3:121431000-121449600	Strong transcription	Liver	Liver
29	chr3:121431000-121450000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:121431000-121450000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:121431200-121448200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:121431400-121448800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:121431400-121449800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:121431400-121450400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:121431600-121441800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr3:121431600-121446000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:121431600-121446600	Strong transcription	HSMMtube	muscle
38	chr3:121431600-121449000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:121432000-121441000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:121432000-121442000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:121432000-121444800	Strong transcription	Brain Anterior Caudate	brain
42	chr3:121432000-121444800	Strong transcription	Fetal Brain Female	brain
43	chr3:121432000-121448200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:121432000-121448400	Strong transcription	HSMM	muscle
45	chr3:121432000-121448800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:121432000-121448800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:121432000-121448800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:121432000-121448800	Strong transcription	NH-A	brain
49	chr3:121432000-121449000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:121432200-121442000	Strong transcription	Stomach Smooth Muscle	stomach

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