Variant report

Variant	rs7536561
Chromosome Location	chr1:180243524-180243525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1043744	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494527	0.85[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.93[MKK][hapmap]
rs10753209	0.89[CHB][hapmap]
rs10753211	0.90[CHB][hapmap]
rs10798745	0.85[CHB][hapmap]
rs10798746	0.90[CHB][hapmap];0.87[YRI][hapmap]
rs10798759	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs10798762	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[MKK][hapmap]
rs10798769	0.82[CHB][hapmap]
rs10913980	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs10913981	0.90[CHB][hapmap]
rs10913984	0.90[CHB][hapmap]
rs10913985	0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[MKK][hapmap]
rs12034217	0.90[CHB][hapmap];0.88[YRI][hapmap]
rs12730889	0.90[CHB][hapmap]
rs1925339	0.90[CHB][hapmap]
rs2290478	0.84[MEX][hapmap]
rs2296378	0.90[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap]
rs2794962	0.85[ASN][1000 genomes]
rs3845397	0.92[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4058058	0.90[CHB][hapmap]
rs4076403	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[MKK][hapmap]
rs4421553	0.90[CHB][hapmap]
rs4442335	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs4578179	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[MKK][hapmap]
rs4651064	0.90[CHB][hapmap]
rs4652493	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs6665719	0.90[CHB][hapmap];0.88[YRI][hapmap]
rs6670544	0.90[CHB][hapmap]
rs716760	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap]
rs7528650	0.90[CHB][hapmap]
rs7532806	0.94[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS 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	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active 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
6	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7536561	LHX4	cis	Thyroid	GTEx
rs7536561	TEDDM1	cis	parietal	SCAN
rs7536561	RGSL1	cis	cerebellum	SCAN
rs7536561	RINT1	trans	cerebellum	SCAN
rs7536561	NCRNA00272	cis	cerebellum	SCAN
rs7536561	ACBD6	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180231000-180257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180236200-180252200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:180236400-180249800	Weak transcription	Hela-S3	cervix
4	chr1:180236800-180257600	Weak transcription	Fetal Brain Male	brain
5	chr1:180237200-180243800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:180237800-180245000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:180238000-180243800	Weak transcription	Fetal Kidney	kidney
8	chr1:180238600-180255600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:180239000-180244400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:180239200-180257200	Weak transcription	Osteobl	bone
11	chr1:180239400-180249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:180239600-180246400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:180240000-180246000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:180240200-180245400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:180240200-180259000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:180240400-180244800	Weak transcription	Right Ventricle	heart
17	chr1:180240400-180245600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:180240400-180246600	Weak transcription	Fetal Thymus	thymus
19	chr1:180240600-180245000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:180240600-180245200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:180240600-180255600	Weak transcription	Liver	Liver
22	chr1:180240800-180243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:180240800-180244800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:180240800-180246400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:180240800-180247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:180240800-180249400	Weak transcription	Left Ventricle	heart
27	chr1:180240800-180258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:180240800-180259400	Weak transcription	HepG2	liver
29	chr1:180240800-180264000	Weak transcription	Small Intestine	intestine
30	chr1:180240800-180270800	Weak transcription	NHLF	lung
31	chr1:180241000-180245200	Weak transcription	Stomach Mucosa	stomach
32	chr1:180241000-180245400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:180241000-180245400	Strong transcription	Fetal Intestine Small	intestine
34	chr1:180241000-180246200	Strong transcription	Fetal Stomach	stomach
35	chr1:180241000-180246400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:180241000-180254800	Weak transcription	HMEC	breast
37	chr1:180241000-180259600	Weak transcription	NH-A	brain
38	chr1:180241200-180243800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:180241200-180257000	Weak transcription	K562	blood
40	chr1:180241400-180244000	Strong transcription	Primary B cells from cord blood	blood
41	chr1:180241400-180247400	Weak transcription	HUVEC	blood vessel
42	chr1:180241400-180247600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:180241400-180247600	Weak transcription	Brain Anterior Caudate	brain
44	chr1:180241400-180250800	Strong transcription	Primary T cells from cord blood	blood
45	chr1:180241600-180245000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:180241600-180247600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:180241600-180251000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:180241800-180243600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:180241800-180244800	Weak transcription	Psoas Muscle	Psoas
50	chr1:180241800-180245600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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