Variant report

Variant	rs8100220
Chromosome Location	chr19:39361658-39361659
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr19:39361194-39361700	HEK293-T-REx	kidney:	n/a	chr19:39361490-39361511 chr19:39361511-39361532
2	CTCF	chr19:39359682-39362626	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39360853..39363331-chr19:39369280..39371226,2	MCF-7	breast:
2	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:
3	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
4	chr19:39361253..39362787-chr19:39366750..39368936,2	MCF-7	breast:
5	chr19:39340592..39344706-chr19:39357882..39361932,6	K562	blood:
6	chr19:39360424..39362257-chr19:39368137..39371034,2	K562	blood:
7	chr19:39321462..39323411-chr19:39359373..39361824,2	MCF-7	breast:
8	chr19:39358481..39361924-chr19:39367868..39369637,3	K562	blood:
9	chr19:39341886..39344706-chr19:39358962..39361932,2	K562	blood:
10	chr19:39360175..39362471-chr19:39419567..39421419,2	MCF-7	breast:

No data

Variant related genes	Relation type
RINL	TF binding region
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1001413	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2113123	0.86[CHB][hapmap]
rs2278009	0.96[CHB][hapmap];0.86[JPT][hapmap]
rs2278011	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs2278012	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs28496951	0.86[CHB][hapmap]
rs6508822	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255774	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs8104420	0.86[CHB][hapmap]
rs862455	1.00[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8100220	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs8100220	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs8100220	HNRNPL	cis	multi-tissue	Pritchard
rs8100220	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39353400-39363800	Weak transcription	HSMMtube	muscle
2	chr19:39356200-39368000	Weak transcription	HepG2	liver
3	chr19:39360000-39361800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39360000-39361800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:39360800-39371400	Weak transcription	NHLF	lung
6	chr19:39360800-39379200	Weak transcription	NHDF-Ad	bronchial
7	chr19:39361000-39361800	Enhancers	Fetal Muscle Trunk	muscle
8	chr19:39361000-39370000	Weak transcription	Aorta	Aorta
9	chr19:39361000-39379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:39361000-39380200	Weak transcription	Psoas Muscle	Psoas
11	chr19:39361200-39361800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39361200-39361800	Enhancers	Primary B cells from cord blood	blood
13	chr19:39361200-39361800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:39361200-39362000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:39361200-39362000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr19:39361200-39363600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:39361200-39363800	Weak transcription	NHEK	skin
18	chr19:39361200-39364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:39361200-39367200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:39361200-39367800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:39361200-39368200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:39361200-39368400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:39361200-39368400	Weak transcription	Stomach Mucosa	stomach
24	chr19:39361200-39368400	Weak transcription	HMEC	breast
25	chr19:39361200-39368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:39361200-39368600	Weak transcription	Gastric	stomach
27	chr19:39361200-39368600	Weak transcription	Right Atrium	heart
28	chr19:39361200-39369200	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:39361200-39369400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:39361200-39369400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:39361200-39369600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:39361200-39369800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:39361200-39369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:39361200-39369800	Weak transcription	Pancreas	Pancrea
35	chr19:39361200-39370000	Weak transcription	Brain Substantia Nigra	brain
36	chr19:39361200-39370400	Weak transcription	Brain Angular Gyrus	brain
37	chr19:39361200-39370600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:39361200-39370800	Weak transcription	Ovary	ovary
39	chr19:39361200-39371000	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:39361200-39371200	Weak transcription	Liver	Liver
41	chr19:39361200-39376800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:39361400-39361800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:39361400-39361800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr19:39361400-39361800	Genic enhancers	Spleen	Spleen
45	chr19:39361400-39362000	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr19:39361400-39362000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:39361400-39362200	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr19:39361400-39363600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:39361400-39364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:39361400-39367000	Weak transcription	Fetal Intestine Large	intestine

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