Variant report

Variant	rs1919554
Chromosome Location	chr3:121447911-121447912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121444248..121448130-chr3:121467032..121469955,4	MCF-7	breast:
2	chr3:121442817..121449533-chr3:121463247..121470201,7	K562	blood:
3	chr3:121445585..121448189-chr3:121448345..121450193,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10511407	0.82[JPT][hapmap]
rs10934556	0.83[AFR][1000 genomes]
rs10934557	0.85[ASN][1000 genomes]
rs10934561	0.82[JPT][hapmap]
rs11915822	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11919421	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11927625	0.86[YRI][hapmap]
rs12486456	0.82[JPT][hapmap]
rs12488717	0.97[ASN][1000 genomes]
rs12489110	0.85[ASN][1000 genomes]
rs12489196	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12489686	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12491109	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12492214	0.82[JPT][hapmap]
rs12493927	1.00[JPT][hapmap]
rs12631803	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12636562	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12637265	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1574654	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1814668	0.84[AFR][1000 genomes]
rs1919553	0.99[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1919556	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1920307	0.82[JPT][hapmap]
rs1971281	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2055034	0.85[AFR][1000 genomes]
rs2700414	0.82[JPT][hapmap]
rs35674179	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35825165	0.99[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3805125	0.83[ASW][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap]
rs3805129	0.82[JPT][hapmap]
rs4048693	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4610269	0.82[JPT][hapmap]
rs55930520	0.85[ASN][1000 genomes]
rs55964762	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56109033	0.85[AFR][1000 genomes]
rs56286202	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6762575	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6766737	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6775634	0.85[ASN][1000 genomes]
rs6786605	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6793556	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6798575	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7643293	1.00[JPT][hapmap];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1919554	HCLS1	cis	lymphoblastoid	seeQTL
rs1919554	HCLS1	cis	multi-tissue	Pritchard
rs1919554	HCLS1	cis	Lymphoblastoid	GTEx
rs1919554	PARP14	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121429000-121450000	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr3:121429400-121448800	Strong transcription	Primary hematopoietic stem cells	blood
3	chr3:121429400-121449000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:121430200-121450000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:121430600-121449000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:121430600-121449400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:121430600-121450000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:121430800-121448200	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:121430800-121448800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:121430800-121448800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:121430800-121450000	Strong transcription	Fetal Intestine Large	intestine
12	chr3:121431000-121448600	Strong transcription	Adipose Nuclei	Adipose
13	chr3:121431000-121449000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:121431000-121449000	Strong transcription	Fetal Thymus	thymus
15	chr3:121431000-121449600	Strong transcription	Liver	Liver
16	chr3:121431000-121450000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:121431000-121450000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:121431200-121448200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:121431400-121448800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:121431400-121449800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr3:121431400-121450400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:121431600-121449000	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr3:121432000-121448200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:121432000-121448400	Strong transcription	HSMM	muscle
25	chr3:121432000-121448800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:121432000-121448800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:121432000-121448800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:121432000-121448800	Strong transcription	NH-A	brain
29	chr3:121432000-121449000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:121432200-121448800	Strong transcription	Fetal Lung	lung
31	chr3:121432400-121448200	Strong transcription	Dnd41	blood
32	chr3:121432400-121449000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:121432600-121449800	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:121434200-121448800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:121435000-121448800	Strong transcription	NHDF-Ad	bronchial
36	chr3:121435200-121449200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:121435200-121449600	Strong transcription	Primary B cells from cord blood	blood
38	chr3:121435400-121448800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:121435600-121448000	Strong transcription	Fetal Kidney	kidney
40	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
41	chr3:121437800-121450000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:121438400-121448800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:121438400-121449800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:121438400-121450000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:121439000-121449000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:121439200-121448800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
48	chr3:121442200-121448800	Strong transcription	Osteobl	bone
49	chr3:121442400-121448600	Strong transcription	Brain Germinal Matrix	brain
50	chr3:121442600-121448800	Strong transcription	Placenta Amnion	Placenta Amnion

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