Variant report

Variant	rs7518099
Chromosome Location	chr1:165736880-165736881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:165736624-165740514	K562	blood:	n/a	n/a
2	HCFC1	chr1:165736860-165738955	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:165736733-165736990	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr1:165736796-165739222	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
2	chr1:165734875..165737199-chr1:165810836..165813345,2	K562	blood:
3	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:
4	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
5	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
6	chr1:165735880..165737855-chr1:165863441..165866125,2	K562	blood:
7	chr1:165667536..165669486-chr1:165736821..165739691,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224358	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000215838	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4233408	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.80[AMR][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Intraocular pressure	24002674	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7518099	ADCY10	cis	parietal	SCAN
rs7518099	MAEL	cis	cerebellum	SCAN
rs7518099	NDUFS2	cis	cerebellum	SCAN
rs7518099	ARHGAP30	cis	parietal	SCAN
rs7518099	FAM78B	cis	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
4	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
6	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
7	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
8	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:165726800-165737000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:165727800-165737000	Weak transcription	Psoas Muscle	Psoas
12	chr1:165727800-165737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:165729200-165737200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:165732200-165737000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:165732200-165737000	Strong transcription	Fetal Thymus	thymus
16	chr1:165732600-165737000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:165732600-165737200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:165732800-165737000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:165732800-165737400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:165733000-165737000	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:165733000-165737200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:165733200-165737000	Strong transcription	Primary B cells from cord blood	blood
23	chr1:165733400-165737000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:165733400-165737000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:165733600-165737000	Strong transcription	Placenta	Placenta
26	chr1:165734000-165737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:165734000-165737000	Genic enhancers	Liver	Liver
28	chr1:165734200-165737000	Strong transcription	Fetal Kidney	kidney
29	chr1:165734400-165737000	Strong transcription	Fetal Stomach	stomach
30	chr1:165734600-165737200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:165734600-165737200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr1:165734800-165737000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:165734800-165737000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:165735200-165737200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:165735400-165737200	Weak transcription	Fetal Lung	lung
36	chr1:165735400-165737400	Weak transcription	Aorta	Aorta
37	chr1:165735600-165737000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:165735600-165737000	Weak transcription	Brain Angular Gyrus	brain
39	chr1:165735600-165737000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:165735800-165737000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:165735800-165737000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:165735800-165737000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:165735800-165737000	Weak transcription	HMEC	breast
44	chr1:165735800-165737000	Genic enhancers	K562	blood
45	chr1:165735800-165737000	Weak transcription	NHLF	lung
46	chr1:165735800-165737200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:165735800-165737200	Weak transcription	HSMMtube	muscle
48	chr1:165735800-165737200	Weak transcription	HUVEC	blood vessel
49	chr1:165735800-165737400	Weak transcription	Left Ventricle	heart
50	chr1:165735800-165737400	Weak transcription	Right Ventricle	heart

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