Variant report

Variant	rs4849050
Chromosome Location	chr2:112939548-112939549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11900153	0.81[CHB][hapmap]
rs12465398	0.81[CHB][hapmap]
rs12711735	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13001618	0.81[CHB][hapmap]
rs13031326	0.80[CHB][hapmap]
rs13387246	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13394408	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13402356	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2312459	0.81[CHB][hapmap]
rs3811643	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848280	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849049	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7557904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591933	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4849050	ZC3H8	cis	parietal	SCAN
rs4849050	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112938000-112939800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:112939000-112939600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:112939000-112939600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:112939000-112939600	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:112939000-112939600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:112939000-112939600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:112939000-112939600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:112939000-112939600	Enhancers	Pancreas	Pancrea
10	chr2:112939000-112939600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:112939000-112939600	Bivalent Enhancer	HUVEC	blood vessel
12	chr2:112939000-112939800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr2:112939000-112939800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:112939000-112939800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:112939000-112940000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr2:112939000-112940000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:112939000-112940000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:112939000-112940000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
19	chr2:112939000-112940400	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr2:112939000-112940600	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr2:112939000-112940600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr2:112939000-112941200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr2:112939000-112941600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr2:112939200-112939600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:112939200-112939600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:112939200-112939600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr2:112939200-112939600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:112939200-112939600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:112939200-112939600	Bivalent/Poised TSS	Colonic Mucosa	Colon
30	chr2:112939200-112939600	Enhancers	Gastric	stomach
31	chr2:112939200-112939600	Bivalent/Poised TSS	NHEK	skin
32	chr2:112939200-112939800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr2:112939200-112939800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:112939200-112939800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:112939200-112939800	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr2:112939200-112939800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:112939200-112940600	Flanking Active TSS	Fetal Thymus	thymus
38	chr2:112939200-112941600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:112939200-112942800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:112939400-112939600	Enhancers	Esophagus	oesophagus
41	chr2:112939400-112939600	Active TSS	Right Ventricle	heart
42	chr2:112939400-112939800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr2:112939400-112939800	Flanking Active TSS	Thymus	Thymus
44	chr2:112939400-112940400	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr2:112939400-112941200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr2:112939400-112941200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr2:112939400-112942000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:112939400-112944400	Weak transcription	Spleen	Spleen

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