Variant report

Variant	rs1374161
Chromosome Location	chr2:114034627-114034628
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	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1110839	0.94[ASW][hapmap]
rs11689813	0.89[CEU][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13001920	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374162	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1466018	0.94[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1491584	0.81[JPT][hapmap]
rs1491585	0.85[JPT][hapmap]
rs1491586	0.81[JPT][hapmap]
rs2863244	0.81[JPT][hapmap]
rs3748916	0.81[ASW][hapmap]
rs4849188	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542127	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707245	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6720637	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726151	0.80[ASN][1000 genomes]
rs6734610	0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs6749645	0.82[EUR][1000 genomes]
rs6753216	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731834	0.81[ASW][hapmap]
rs7560701	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs895418	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs902695	0.81[ASW][hapmap]
rs902696	0.81[ASW][hapmap]
rs982909	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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1374161	LOC654433	cis	cerebellum	SCAN
rs1374161	RP11-65I12.1	cis	Thyroid	GTEx
rs1374161	AC016683.6	cis	Muscle Skeletal	GTEx
rs1374161	AC016683.6	cis	Whole Blood	GTEx
rs1374161	AC016683.6	cis	Nerve Tibial	GTEx
rs1374161	RFC4	trans	cerebellum	SCAN
rs1374161	AC016683.6	cis	Artery Tibial	GTEx
rs1374161	LOC654433	cis	parietal	SCAN
rs1374161	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs1374161	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs1374161	PAX8	cis	lymphoblastoid	seeQTL
rs1374161	PAX8	cis	parietal	SCAN
rs1374161	PAX8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114023200-114039800	Weak transcription	Gastric	stomach
2	chr2:114031600-114037000	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr2:114032600-114035000	Weak transcription	Right Atrium	heart
4	chr2:114032800-114035800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
5	chr2:114033000-114034800	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr2:114033000-114035400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr2:114033000-114035800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr2:114033000-114036600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:114033000-114038000	Weak transcription	A549	lung
10	chr2:114033200-114034800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr2:114033200-114034800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:114033200-114035000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
13	chr2:114033200-114035000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:114033200-114035400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:114033200-114036000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr2:114033400-114034800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:114033400-114034800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:114033400-114035000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
19	chr2:114033400-114035000	Bivalent Enhancer	Left Ventricle	heart
20	chr2:114033400-114035600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:114033400-114035600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:114033400-114035600	Bivalent Enhancer	Spleen	Spleen
23	chr2:114033400-114036000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:114033400-114036000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr2:114033400-114036400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:114033400-114036400	Bivalent Enhancer	Fetal Brain Male	brain
27	chr2:114033400-114036600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr2:114033600-114036000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
29	chr2:114033600-114036400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:114033600-114036400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:114033600-114037200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:114033800-114035400	Bivalent Enhancer	Stomach Mucosa	stomach
33	chr2:114034000-114036200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:114034200-114034800	Bivalent Enhancer	Fetal Brain Female	brain
35	chr2:114034200-114036600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr2:114034200-114036600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:114034400-114034800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr2:114034400-114034800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr2:114034400-114034800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:114034400-114034800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:114034400-114034800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:114034400-114034800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
43	chr2:114034400-114034800	Bivalent Enhancer	NHEK	skin
44	chr2:114034400-114035000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
45	chr2:114034400-114035200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
46	chr2:114034400-114035200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr2:114034400-114035400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:114034400-114035400	Bivalent Enhancer	Brain Anterior Caudate	brain
49	chr2:114034400-114035600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr2:114034400-114035600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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