Variant report

Variant	rs4251842
Chromosome Location	chr19:44166187-44166188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44165749-44166418	U87	brain:	n/a	n/a
2	POLR2A	chr19:44165850-44166200	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:44165743-44166424	U87	brain:	n/a	n/a
4	POLR2A	chr19:44165815-44166435	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44164779..44167339-chr19:44169033..44171998,3	MCF-7	breast:
2	chr19:44099351..44101191-chr19:44163973..44166677,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL368P	TF binding region
PLAUR	TF binding region
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000011422	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs25491	1.00[ASW][hapmap]
rs3213259	1.00[ASW][hapmap]
rs3213325	1.00[CHD][hapmap]
rs4760	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4251842	LRRC31	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44145000-44167400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr19:44145000-44168000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr19:44145000-44171400	Weak transcription	Fetal Heart	heart
4	chr19:44145000-44171600	Weak transcription	Esophagus	oesophagus
5	chr19:44145400-44171200	Weak transcription	Fetal Brain Female	brain
6	chr19:44149200-44169400	Weak transcription	Fetal Intestine Large	intestine
7	chr19:44150000-44167800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:44150000-44171800	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr19:44150200-44171400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:44150200-44171600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:44150400-44171400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:44150400-44171400	Strong transcription	NH-A	brain
13	chr19:44150400-44171600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:44150400-44171600	Strong transcription	Osteobl	bone
15	chr19:44151000-44167200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:44151000-44171000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:44151600-44171200	Weak transcription	Fetal Lung	lung
18	chr19:44151800-44171600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr19:44155600-44168400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:44155600-44171600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:44155600-44171800	Strong transcription	NHEK	skin
22	chr19:44156000-44168000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:44156000-44171200	Strong transcription	NHLF	lung
24	chr19:44156400-44171400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:44156600-44167800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:44156600-44168800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:44156600-44169400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:44156600-44171200	Weak transcription	K562	blood
29	chr19:44156600-44171400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:44156600-44171400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:44156600-44171600	Weak transcription	Brain Angular Gyrus	brain
32	chr19:44156600-44171600	Weak transcription	Brain Hippocampus Middle	brain
33	chr19:44156600-44171800	Weak transcription	Stomach Mucosa	stomach
34	chr19:44156800-44168800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:44156800-44171400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:44156800-44171400	Weak transcription	Brain Anterior Caudate	brain
37	chr19:44158600-44166200	Strong transcription	HMEC	breast
38	chr19:44158800-44170400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:44159000-44169400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:44159000-44171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:44159800-44168800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:44159800-44169000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:44159800-44169000	Weak transcription	Small Intestine	intestine
44	chr19:44159800-44171200	Weak transcription	Right Ventricle	heart
45	chr19:44159800-44171400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:44160000-44171400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:44160200-44167400	Weak transcription	HUVEC	blood vessel
48	chr19:44160200-44167600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr19:44160200-44168000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:44160200-44171600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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