Variant report

Variant	rs9988459
Chromosome Location	chr1:150899418-150899419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:150898486-150899465	A549	lung:	n/a	n/a
2	HCFC1	chr1:150898193-150899574	Hela-S3	cervix:	n/a	n/a
3	MAX	chr1:150897569-150899436	MCF-7	breast:	n/a	chr1:150898688-150898699 chr1:150899053-150899063
4	IRF1	chr1:150898620-150899432	K562	blood:	n/a	chr1:150899103-150899117 chr1:150898656-150898670
5	TCF12	chr1:150898333-150899446	A549	lung:	n/a	n/a
6	POLR2A	chr1:150898275-150899497	HUVEC	blood vessel:	n/a	n/a
7	UBTF	chr1:150899283-150899442	K562	blood:	n/a	n/a
8	MTA3	chr1:150898343-150899504	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:150898327-150899472	SK-N-MC	brain:	n/a	n/a
10	PML	chr1:150898422-150899473	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr1:150898513-150899425	GM12878	blood:	n/a	n/a
12	GABPA	chr1:150898293-150899505	A549	lung:	n/a	chr1:150899104-150899113 chr1:150898719-150898730
13	MXI1	chr1:150898260-150899713	IMR90	lung:	n/a	n/a
14	CHD1	chr1:150898925-150899603	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr1:150898162-150899467	MCF-7	breast:	n/a	chr1:150898688-150898699 chr1:150899053-150899063
16	GABPA	chr1:150898172-150899786	MCF-7	breast:	n/a	chr1:150899104-150899113 chr1:150898719-150898730
17	POLR2A	chr1:150898480-150899485	HUVEC	blood vessel:	n/a	n/a
18	CUX1	chr1:150899279-150899471	GM12878	blood:	n/a	n/a
19	SIX5	chr1:150898404-150899578	A549	lung:	n/a	n/a
20	POLR2A	chr1:150898349-150899514	SK-N-SH	brain:	n/a	n/a
21	MAX	chr1:150898377-150899421	HCT-116	colon:	n/a	chr1:150898688-150898699 chr1:150899053-150899063
22	MXI1	chr1:150898192-150899802	SK-N-SH	brain:	n/a	n/a
23	YY1	chr1:150898530-150899448	SK-N-SH_RA	brain:	n/a	chr1:150899104-150899113 chr1:150899191-150899201 chr1:150899189-150899201
24	IRF1	chr1:150898459-150899567	K562	blood:	n/a	chr1:150899434-150899444 chr1:150899430-150899444 chr1:150899103-150899117 chr1:150898656-150898670

No.	Distal block	Cell Line	Cell type
1	chr1:150847391..150850807-chr1:150896212..150900555,5	MCF-7	breast:
2	chr1:150541549..150544184-chr1:150897269..150900025,2	K562	blood:
3	chr1:150847503..150849791-chr1:150897618..150900781,3	K562	blood:
4	chr1:150897581..150900279-chr1:150934565..150936945,2	K562	blood:
5	chr1:150848716..150851402-chr1:150897221..150900291,3	MCF-7	breast:
6	chr1:150897692..150900384-chr1:150944923..150947345,3	K562	blood:
7	chr1:150898462..150900740-chr1:151030523..151033024,2	MCF-7	breast:

Variant related genes	Relation type
SETDB1	TF binding region
ENSG00000231073	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10157132	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10305679	0.81[YRI][hapmap]
rs12090632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097548	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16827772	0.85[YRI][hapmap]
rs16832391	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832604	0.89[YRI][hapmap]
rs41496050	0.82[YRI][hapmap]
rs55884154	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56341880	0.89[AMR][1000 genomes]
rs57376891	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57378704	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57734108	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57746902	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58338969	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59687612	0.87[AMR][1000 genomes]
rs59703669	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60676022	0.87[AMR][1000 genomes]
rs6672625	1.00[AMR][1000 genomes]
rs6674452	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703303	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127060	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127063	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127089	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127091	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127092	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74128604	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74128609	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7522741	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547614	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9325979	0.83[YRI][hapmap]
rs9988521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv947130	chr1:150878115-150899504	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150897400-150899800	Active TSS	Fetal Kidney	kidney
2	chr1:150897600-150899600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:150897600-150899600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:150897600-150899600	Active TSS	Fetal Intestine Large	intestine
5	chr1:150897600-150899600	Active TSS	Fetal Intestine Small	intestine
6	chr1:150897600-150899600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:150897600-150899600	Active TSS	Ovary	ovary
8	chr1:150897600-150899600	Active TSS	Pancreas	Pancrea
9	chr1:150897600-150899600	Active TSS	Psoas Muscle	Psoas
10	chr1:150897600-150899600	Active TSS	Right Ventricle	heart
11	chr1:150897600-150899600	Active TSS	Thymus	Thymus
12	chr1:150897600-150899800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:150897600-150899800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:150897600-150900000	Active TSS	NH-A	brain
15	chr1:150897800-150899600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:150897800-150899600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:150897800-150899800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:150897800-150899800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:150897800-150899800	Active TSS	GM12878-XiMat	blood
20	chr1:150897800-150899800	Active TSS	Osteobl	bone
21	chr1:150897800-150900000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:150898000-150899600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:150898000-150899600	Active TSS	Stomach Mucosa	stomach
24	chr1:150898000-150899600	Active TSS	HepG2	liver
25	chr1:150898000-150899800	Active TSS	Fetal Brain Female	brain
26	chr1:150898000-150899800	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:150898000-150900000	Active TSS	Colonic Mucosa	Colon
28	chr1:150898200-150899600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:150898200-150899600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:150898200-150899600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:150898200-150899600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:150898200-150899600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:150898200-150899600	Active TSS	Aorta	Aorta
34	chr1:150898200-150899600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:150898200-150899600	Active TSS	Brain Substantia Nigra	brain
36	chr1:150898200-150899600	Active TSS	Fetal Muscle Leg	muscle
37	chr1:150898200-150899600	Active TSS	Fetal Stomach	stomach
38	chr1:150898200-150899600	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:150898200-150899600	Active TSS	Right Atrium	heart
40	chr1:150898200-150899600	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:150898200-150899600	Active TSS	NHDF-Ad	bronchial
42	chr1:150898200-150899800	Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:150898200-150899800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:150898200-150899800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:150898200-150899800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:150898200-150899800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:150898200-150899800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:150898200-150899800	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:150898200-150899800	Active TSS	HSMM	muscle
50	chr1:150898200-150899800	Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links