Variant report

Variant	rs4233238
Chromosome Location	chr1:224179439-224179440
allele	A/C
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	POLR2A	chr1:224178488-224181742	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr1:224179400-224179700	K562	blood:	n/a	n/a
3	POLR2A	chr1:224178929-224180943	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:224179010-224179461	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:224179134-224179469	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:224178787-224181394	GM12892	blood:	n/a	n/a
7	NR2F2	chr1:224179427-224181073	K562	blood:	n/a	n/a
8	POLR2A	chr1:224178994-224179682	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:224179402-224181020	H1-hESC	embryonic stem cell:	n/a	n/a
10	HEY1	chr1:224179277-224181085	HepG2	liver:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
11	HEY1	chr1:224178955-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
12	PAX5	chr1:224179228-224181319	GM12878	blood:	n/a	n/a
13	HEY1	chr1:224178879-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
14	CTCF	chr1:224179412-224179726	K562	blood:	n/a	n/a
15	POLR2A	chr1:224178883-224181083	GM12878	blood:	n/a	n/a
16	CTCF	chr1:224179325-224181033	K562	blood:	n/a	n/a
17	POLR2A	chr1:224179362-224181605	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr1:224178829-224181509	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:224179005-224180945	GM12891	blood:	n/a	n/a
20	POU2F2	chr1:224178930-224181599	GM12878	blood:	n/a	n/a
21	CBX3	chr1:224179390-224179770	K562	blood:	n/a	n/a
22	PAX5	chr1:224179347-224179645	GM12878	blood:	n/a	n/a
23	TAF1	chr1:224179415-224181129	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:224178915-224181048	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:224179271-224181047	Hela-S3	cervix:	n/a	n/a
26	PAX5	chr1:224179401-224179633	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:224179002-224180944	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:224178995-224180868	GM12891	blood:	n/a	n/a
29	ZBTB33	chr1:224179412-224179674	K562	blood:	n/a	n/a
30	POLR2A	chr1:224178996-224179662	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr1:224178716-224181850	H1-hESC	embryonic stem cell:	n/a	n/a
32	POU2F2	chr1:224179004-224180914	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:224178738-224182255	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:224178886-224181322	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223887763..223889342-chr1:224178879..224180474,2	K562	blood:
2	chr1:224178733..224180652-chr1:224310129..224312087,2	K562	blood:
3	chr1:224178905..224181889-chr1:224301318..224303879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243000	TF binding region
ENSG00000185495	TF binding region
ENSG00000232372	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10753432	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10799376	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10916081	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799993	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11800372	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11825	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12121620	0.82[AMR][1000 genomes]
rs12562032	0.84[AMR][1000 genomes]
rs12568004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2404851	0.84[AMR][1000 genomes]
rs3991971	0.84[AMR][1000 genomes]
rs59220538	0.84[AMR][1000 genomes]
rs61823277	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61823286	0.86[AMR][1000 genomes]
rs61823340	0.84[AMR][1000 genomes]
rs61825422	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825443	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61826582	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61826584	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61826596	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61826599	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61826602	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61826603	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61826608	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61826609	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826610	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689080	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71524984	0.83[ASN][1000 genomes]
rs72629693	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9219	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873215	chr1:224075483-224204433	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1802502	chr1:224076065-224184733	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv873217	chr1:224089383-224190316	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv15701	chr1:224096726-224179951	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv873218	chr1:224097155-224204433	Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv873221	chr1:224115297-224183599	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv549242	chr1:224115297-224203918	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv945316	chr1:224133366-224196526	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv947070	chr1:224178779-224183075	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4233238	RP11-504P24.6	cis	Thyroid	GTEx
rs4233238	RP11-504P24.6	cis	Nerve Tibial	GTEx
rs4233238	RP11-504P24.4	cis	Nerve Tibial	GTEx
rs4233238	RP11-504P24.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4233238	RP11-504P24.3	cis	Nerve Tibial	GTEx
rs4233238	RP11-504P24.4	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224136400-224179800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224138000-224179600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:224138200-224179600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:224138200-224179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:224138400-224179600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:224138400-224179800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:224138600-224179600	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:224138800-224179800	Weak transcription	Left Ventricle	heart
9	chr1:224139800-224179600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224140200-224179800	Weak transcription	Placenta	Placenta
11	chr1:224140400-224179800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:224145000-224179800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:224146800-224179600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:224150000-224179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:224150000-224179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:224150200-224179800	Weak transcription	Liver	Liver
17	chr1:224158000-224179800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:224161400-224179600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:224161600-224179800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:224162200-224179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:224168800-224179800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:224170600-224179600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:224173600-224179800	Weak transcription	Fetal Stomach	stomach
24	chr1:224176000-224180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:224177000-224179600	Weak transcription	HSMM	muscle
26	chr1:224179000-224179600	Enhancers	Pancreas	Pancrea
27	chr1:224179000-224179600	Enhancers	Dnd41	blood
28	chr1:224179000-224179600	Enhancers	K562	blood
29	chr1:224179000-224182200	Active TSS	GM12878-XiMat	blood
30	chr1:224179200-224179600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:224179200-224179600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:224179200-224179600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:224179200-224179600	Enhancers	Brain Anterior Caudate	brain
34	chr1:224179200-224179600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:224179200-224179600	Enhancers	Ovary	ovary
36	chr1:224179200-224179600	Enhancers	HepG2	liver
37	chr1:224179200-224179800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:224179200-224181800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:224179400-224179600	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:224179400-224179600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:224179400-224179600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:224179400-224179800	Weak transcription	Psoas Muscle	Psoas
43	chr1:224179400-224179800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:224179400-224181400	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr1:224179400-224182200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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