Variant report

Variant	rs2113123
Chromosome Location	chr19:39312231-39312232
allele	C/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	REST	chr19:39311923-39312532	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39312112-39312522	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:39302778-39313143	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
ECH1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001413	0.91[CHB][hapmap]
rs10411844	0.97[ASN][1000 genomes]
rs1103435	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11668179	0.86[JPT][hapmap]
rs11671711	0.85[JPT][hapmap]
rs2113124	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278009	0.95[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes]
rs2278011	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2278012	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2318459	0.99[EUR][1000 genomes]
rs28496951	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35812434	0.82[EUR][1000 genomes]
rs6508822	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs67859595	0.93[EUR][1000 genomes]
rs7246134	0.99[EUR][1000 genomes]
rs7248208	0.81[JPT][hapmap]
rs7255774	0.90[CEU][hapmap];0.91[CHB][hapmap]
rs8100220	0.86[CHB][hapmap]
rs8104416	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862455	0.84[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs862459	0.95[EUR][1000 genomes]
rs862464	0.91[EUR][1000 genomes]
rs9419	0.85[JPT][hapmap]
rs9789283	0.88[EUR][1000 genomes]

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	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2113123	SUPT5H	cis	brain	BrainEAC
rs2113123	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs2113123	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs2113123	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
2	chr19:39296200-39318200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39296400-39318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:39296400-39318200	Weak transcription	NHEK	skin
5	chr19:39301400-39320200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:39304000-39317600	Weak transcription	HSMMtube	muscle
7	chr19:39304200-39312800	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:39304400-39316800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:39304600-39318200	Weak transcription	Osteobl	bone
11	chr19:39304800-39320800	Weak transcription	HSMM	muscle
12	chr19:39305000-39315000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr19:39305200-39316000	Strong transcription	Primary T cells from cord blood	blood
14	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
15	chr19:39305400-39315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:39305600-39314000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:39305600-39314000	Strong transcription	Esophagus	oesophagus
19	chr19:39305600-39314000	Strong transcription	Lung	lung
20	chr19:39305600-39314400	Strong transcription	Thymus	Thymus
21	chr19:39305600-39318800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr19:39305600-39320400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:39305800-39312600	Strong transcription	Fetal Brain Female	brain
25	chr19:39305800-39312800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:39305800-39313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:39306400-39317800	Weak transcription	Small Intestine	intestine
28	chr19:39307400-39321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:39308000-39313400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39308000-39317600	Weak transcription	Fetal Thymus	thymus
31	chr19:39308200-39313400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:39308200-39313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:39308200-39320400	Weak transcription	NHLF	lung
34	chr19:39308400-39314000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:39308400-39315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:39308400-39318200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39308600-39314600	Weak transcription	Primary B cells from cord blood	blood
38	chr19:39308600-39318000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:39308800-39313400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:39308800-39313600	Weak transcription	Brain Substantia Nigra	brain
41	chr19:39308800-39316600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:39308800-39318200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:39309000-39313400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:39309000-39313400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:39309000-39313400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:39309000-39313400	Weak transcription	GM12878-XiMat	blood
47	chr19:39309000-39313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:39309000-39318000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:39309000-39318000	Weak transcription	Brain Angular Gyrus	brain
50	chr19:39309000-39318200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links