Variant report

Variant	rs697847
Chromosome Location	chr1:226864958-226864959
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	GATA3	chr1:226864631-226865302	SK-N-SH	brain:	n/a	n/a
2	FOS	chr1:226864736-226865128	MCF10A-Er-Src	breast:	n/a	n/a
3	FOSL2	chr1:226864563-226865223	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:226864945-226865148	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOS	chr1:226864667-226865175	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF12	chr1:226864541-226865391	SK-N-SH	brain:	n/a	chr1:226864854-226864864
7	POLR2A	chr1:226864725-226865155	SK-N-SH	brain:	n/a	n/a
8	RCOR1	chr1:226864603-226865323	IMR90	lung:	n/a	n/a
9	EBF1	chr1:226864818-226865244	GM12878	blood:	n/a	chr1:226864848-226864857
10	EBF1	chr1:226864843-226865186	GM12878	blood:	n/a	chr1:226864848-226864857
11	GATA3	chr1:226864706-226865388	SK-N-SH	brain:	n/a	n/a
12	MEF2A	chr1:226864640-226865331	SK-N-SH	brain:	n/a	chr1:226864998-226865019 chr1:226865003-226865012 chr1:226864998-226865019 chr1:226865002-226865013 chr1:226865000-226865015
13	E2F4	chr1:226864949-226865129	MCF10A-Er-Src	breast:	n/a	n/a
14	MEF2A	chr1:226864553-226865390	SK-N-SH	brain:	n/a	chr1:226864998-226865019 chr1:226865003-226865012 chr1:226864998-226865019 chr1:226864600-226864615 chr1:226865002-226865013 chr1:226865000-226865015
15	MAX	chr1:226864909-226865587	NB4	blood:	n/a	n/a
16	RAD21	chr1:226864837-226865175	IMR90	lung:	n/a	n/a
17	IKZF1	chr1:226864102-226865360	GM12878	blood:	n/a	n/a
18	MAFK	chr1:226864799-226865093	IMR90	lung:	n/a	n/a
19	RUNX3	chr1:226864831-226865325	GM12878	blood:	n/a	n/a
20	FOXA1	chr1:226864762-226865183	T-47D	breast:	n/a	n/a
21	TEAD4	chr1:226864601-226865233	SK-N-SH	brain:	n/a	n/a
22	FOXA1	chr1:226864622-226865190	T-47D	breast:	n/a	n/a
23	FOS	chr1:226864424-226865209	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr1:226864787-226865240	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr1:226864659-226865193	SK-N-SH	brain:	n/a	n/a
26	MAX	chr1:226864688-226865282	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:226864596-226865127	MCF10A-Er-Src	breast:	n/a	n/a
28	RXRA	chr1:226864700-226865307	SK-N-SH	brain:	n/a	n/a
29	MTA3	chr1:226864610-226865413	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:226864865-226865124	H1-hESC	embryonic stem cell:	n/a	n/a
31	STAT3	chr1:226864683-226865108	MCF10A-Er-Src	breast:	n/a	chr1:226865069-226865077
32	NFIC	chr1:226864620-226865281	SK-N-SH	brain:	n/a	n/a
33	JUND	chr1:226864657-226865268	SK-N-SH	brain:	n/a	n/a
34	SPI1	chr1:226864879-226865464	HL-60	blood:	n/a	chr1:226865091-226865104
35	RUNX3	chr1:226864849-226865430	GM12878	blood:	n/a	n/a
36	STAT3	chr1:226864679-226865149	MCF10A-Er-Src	breast:	n/a	chr1:226865069-226865077
37	EP300	chr1:226864516-226865200	T-47D	breast:	n/a	chr1:226864603-226864617
38	MYC	chr1:226864784-226865218	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr1:226864687-226865209	MCF10A-Er-Src	breast:	n/a	n/a
40	RELA	chr1:226864903-226865368	GM18951	blood:	n/a	n/a
41	EBF1	chr1:226864725-226865350	GM12878	blood:	n/a	chr1:226864848-226864857
42	SIN3AK20	chr1:226864798-226865126	SK-N-SH	brain:	n/a	n/a
43	REST	chr1:226864732-226865169	SK-N-SH	brain:	n/a	chr1:226864848-226864861 chr1:226864848-226864861 chr1:226864742-226864755
44	GATA3	chr1:226864644-226865163	T-47D	breast:	n/a	n/a
45	POLR2A	chr1:226864755-226865455	HL-60	blood:	n/a	n/a
46	POLR2A	chr1:226864812-226865691	HL-60	blood:	n/a	n/a
47	NFIC	chr1:226864714-226865270	GM12878	blood:	n/a	n/a
48	STAT3	chr1:226864712-226865176	MCF10A-Er-Src	breast:	n/a	chr1:226865069-226865077
49	STAT3	chr1:226864679-226865210	MCF10A-Er-Src	breast:	n/a	chr1:226865069-226865077
50	ZNF143	chr1:226864954-226865235	GM12878	blood:	n/a	n/a

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	chr1:226864917..226867492-chr1:226868629..226873346,4	K562	blood:
4	chr1:226858880..226860539-chr1:226862980..226865164,2	K562	blood:
5	chr1:226863575..226866275-chr1:226866512..226868016,2	MCF-7	breast:

Variant related genes	Relation type
ITPKB-IT1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1070361	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1071530	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1288936	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1288938	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1288939	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768393	1.00[ASN][1000 genomes]
rs3768396	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820640	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs708766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	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:114 , 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	chr1:226860600-226865200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:226860600-226867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:226860600-226867600	Weak transcription	Gastric	stomach
9	chr1:226860800-226867400	Weak transcription	Fetal Intestine Large	intestine
10	chr1:226860800-226867400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:226861600-226865600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:226861600-226866800	Enhancers	Psoas Muscle	Psoas
13	chr1:226861600-226867400	Enhancers	Fetal Muscle Leg	muscle
14	chr1:226862200-226866800	Enhancers	Lung	lung
15	chr1:226862400-226865600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:226862400-226865600	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:226862400-226865800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:226862400-226866000	Enhancers	NHDF-Ad	bronchial
19	chr1:226862400-226866800	Enhancers	Right Atrium	heart
20	chr1:226862400-226867000	Enhancers	Spleen	Spleen
21	chr1:226862400-226867600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:226862400-226867600	Enhancers	Placenta	Placenta
23	chr1:226862400-226868400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:226862600-226865600	Enhancers	NHLF	lung
25	chr1:226862600-226865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:226862600-226866200	Enhancers	Esophagus	oesophagus
27	chr1:226862600-226867200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:226862600-226867400	Enhancers	Brain Angular Gyrus	brain
29	chr1:226862600-226867600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:226862800-226866400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:226863000-226865800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:226863000-226866000	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr1:226863000-226866800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:226863000-226867800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr1:226863200-226865400	Enhancers	Stomach Mucosa	stomach
36	chr1:226863200-226866800	Genic enhancers	Fetal Thymus	thymus
37	chr1:226863200-226867600	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr1:226863400-226865800	Enhancers	Fetal Stomach	stomach
39	chr1:226863400-226867000	Enhancers	Right Ventricle	heart
40	chr1:226863400-226867400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:226863600-226865000	Enhancers	Adipose Nuclei	Adipose
42	chr1:226863600-226865600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:226863600-226866800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:226863600-226867000	Weak transcription	Fetal Lung	lung
45	chr1:226863600-226867400	Weak transcription	Fetal Kidney	kidney
46	chr1:226863800-226865800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr1:226863800-226867000	Enhancers	Dnd41	blood
48	chr1:226864000-226865000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:226864000-226865600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr1:226864000-226865600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links