Variant report

Variant	rs4653461
Chromosome Location	chr1:226865514-226865515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:226864909-226865587	NB4	blood:	n/a	n/a
2	CTCF	chr1:226865460-226865610	HBMEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:226864812-226865691	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226864917..226866884-chr1:226868100..226871098,3	K562	blood:
2	chr1:226848680..226852398-chr1:226863556..226867477,3	MCF-7	breast:
3	chr1:226837244..226840102-chr1:226865021..226866969,2	MCF-7	breast:
4	chr1:226864917..226867492-chr1:226868629..226873346,4	K562	blood:
5	chr1:226863575..226866275-chr1:226866512..226868016,2	MCF-7	breast:

No data

Variant related genes	Relation type
ITPKB-IT1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12095028	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846351	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs16846357	1.00[ASN][1000 genomes]
rs16846378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754398	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754399	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754401	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754403	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3754407	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3754409	0.89[JPT][hapmap]
rs3754413	0.82[ASN][1000 genomes]
rs3768388	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768389	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768397	1.00[ASN][1000 genomes]
rs3768400	1.00[ASN][1000 genomes]
rs3768416	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs3820641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820647	0.82[ASN][1000 genomes]
rs4653464	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs56095953	0.82[ASN][1000 genomes]
rs58091460	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58755194	0.90[AFR][1000 genomes]
rs73100937	0.93[AFR][1000 genomes]
rs73100938	0.93[AFR][1000 genomes]
rs73100939	0.93[AFR][1000 genomes]
rs73100942	0.91[AFR][1000 genomes]
rs7524854	0.91[AMR][1000 genomes];0.93[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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226856200-226867400	Weak transcription	Fetal Brain Female	brain
2	chr1:226856200-226868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:226859600-226867600	Enhancers	Colon Smooth Muscle	Colon
4	chr1:226860200-226867000	Enhancers	Left Ventricle	heart
5	chr1:226860400-226866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:226860600-226867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:226860600-226867600	Weak transcription	Gastric	stomach
8	chr1:226860800-226867400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:226860800-226867400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:226861600-226865600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:226861600-226866800	Enhancers	Psoas Muscle	Psoas
12	chr1:226861600-226867400	Enhancers	Fetal Muscle Leg	muscle
13	chr1:226862200-226866800	Enhancers	Lung	lung
14	chr1:226862400-226865600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:226862400-226865600	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:226862400-226865800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:226862400-226866000	Enhancers	NHDF-Ad	bronchial
18	chr1:226862400-226866800	Enhancers	Right Atrium	heart
19	chr1:226862400-226867000	Enhancers	Spleen	Spleen
20	chr1:226862400-226867600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:226862400-226867600	Enhancers	Placenta	Placenta
22	chr1:226862400-226868400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr1:226862600-226865600	Enhancers	NHLF	lung
24	chr1:226862600-226865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:226862600-226866200	Enhancers	Esophagus	oesophagus
26	chr1:226862600-226867200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:226862600-226867400	Enhancers	Brain Angular Gyrus	brain
28	chr1:226862600-226867600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:226862800-226866400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:226863000-226865800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr1:226863000-226866000	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr1:226863000-226866800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:226863000-226867800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr1:226863200-226866800	Genic enhancers	Fetal Thymus	thymus
35	chr1:226863200-226867600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:226863400-226865800	Enhancers	Fetal Stomach	stomach
37	chr1:226863400-226867000	Enhancers	Right Ventricle	heart
38	chr1:226863400-226867400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:226863600-226865600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:226863600-226866800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:226863600-226867000	Weak transcription	Fetal Lung	lung
42	chr1:226863600-226867400	Weak transcription	Fetal Kidney	kidney
43	chr1:226863800-226865800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:226863800-226867000	Enhancers	Dnd41	blood
45	chr1:226864000-226865600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr1:226864000-226865600	Enhancers	HMEC	breast
47	chr1:226864000-226865600	Enhancers	HSMMtube	muscle
48	chr1:226864000-226865800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:226864000-226865800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:226864000-226866200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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