Variant report

Variant	rs4968253
Chromosome Location	chr17:45170919-45170920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45169541..45171629-chr17:45172586..45174850,2	K562	blood:
2	chr17:45170129..45171669-chr17:45173350..45174934,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10514915	0.95[ASN][1000 genomes]
rs11079748	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079750	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079752	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649887	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654517	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658350	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871052	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11871364	0.87[EUR][1000 genomes]
rs12603447	0.91[ASN][1000 genomes]
rs12939753	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12942936	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949929	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12950276	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950699	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1634260	0.95[ASN][1000 genomes]
rs2007723	0.90[ASN][1000 genomes]
rs2316331	0.93[ASN][1000 genomes]
rs2317376	0.95[ASN][1000 genomes]
rs2873131	0.95[ASN][1000 genomes]
rs34038545	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34314554	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34710835	0.96[ASN][1000 genomes]
rs35721448	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4074247	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074249	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968301	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968304	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56362502	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7207418	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214785	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7215573	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215903	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215907	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219544	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219899	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220777	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7222781	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8077021	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889451	0.91[ASN][1000 genomes]
rs9899078	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
6	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4968253	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:45145000-45176800	Weak transcription	Lung	lung
4	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
6	chr17:45148800-45175400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:45149000-45173800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:45149600-45175400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr17:45149600-45176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:45150200-45174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:45150600-45176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:45150600-45176800	Weak transcription	Left Ventricle	heart
13	chr17:45155600-45173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr17:45158600-45175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:45159200-45175600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr17:45163200-45176800	Weak transcription	Fetal Intestine Large	intestine
17	chr17:45163800-45175000	Weak transcription	HepG2	liver
18	chr17:45164600-45174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:45164800-45176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr17:45166200-45176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:45167600-45177000	Weak transcription	Spleen	Spleen
22	chr17:45168400-45176000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:45168400-45176800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr17:45168600-45171000	Enhancers	Primary B cells from peripheral blood	blood
25	chr17:45168600-45176200	Weak transcription	NH-A	brain
26	chr17:45168800-45176800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:45169000-45171000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr17:45169200-45176200	Weak transcription	Adipose Nuclei	Adipose
29	chr17:45169800-45171000	ZNF genes & repeats	Fetal Brain Female	brain
30	chr17:45169800-45171000	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr17:45169800-45171000	ZNF genes & repeats	Fetal Lung	lung
32	chr17:45169800-45171000	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr17:45169800-45171000	ZNF genes & repeats	Fetal Thymus	thymus
34	chr17:45169800-45171600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:45169800-45171600	ZNF genes & repeats	Fetal Stomach	stomach
36	chr17:45170000-45171000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr17:45170000-45171000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:45170000-45171000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
39	chr17:45170000-45174600	Weak transcription	Primary B cells from cord blood	blood
40	chr17:45170200-45171000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:45170200-45171000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:45170200-45171000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:45170200-45171000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr17:45170200-45171000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr17:45170200-45171000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:45170200-45171000	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr17:45170200-45171000	ZNF genes & repeats	Psoas Muscle	Psoas
48	chr17:45170200-45171000	Strong transcription	NHEK	skin
49	chr17:45170200-45176800	Weak transcription	Aorta	Aorta
50	chr17:45170400-45171000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links