Variant report

Variant	rs5749131
Chromosome Location	chr22:31001822-31001823
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	ELF1	chr22:31001515-31001871	HepG2	liver:	n/a	n/a
2	CTCF	chr22:31001586-31001841	Spleen_OC	spleen:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
3	FOXM1	chr22:31001473-31001930	GM12878	blood:	n/a	n/a
4	SMC3	chr22:31001551-31001868	HepG2	liver:	n/a	chr22:31001697-31001711
5	CTCF	chr22:31001592-31001832	HepG2	liver:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
6	ELF1	chr22:31001403-31001915	K562	blood:	n/a	n/a
7	SP4	chr22:31001507-31001966	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr22:31001634-31001884	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr22:31001513-31001865	HCT-116	colon:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
10	HCFC1	chr22:31001452-31001925	K562	blood:	n/a	n/a
11	MAX	chr22:31001577-31002044	A549	lung:	n/a	n/a
12	CTCF	chr22:31001523-31001890	H1-hESC	embryonic stem cell:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
13	CTCF	chr22:31001551-31001872	K562	blood:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
14	POLR2A	chr22:31001515-31001925	HCT-116	colon:	n/a	n/a
15	MAX	chr22:31001572-31001907	NB4	blood:	n/a	n/a
16	MAZ	chr22:31001535-31001870	GM12878	blood:	n/a	n/a
17	MAX	chr22:31001371-31002115	A549	lung:	n/a	n/a
18	BHLHE40	chr22:31001466-31001893	K562	blood:	n/a	n/a
19	ELF1	chr22:31001384-31001970	MCF-7	breast:	n/a	n/a
20	CTCF	chr22:31001329-31002060	HCT-116	colon:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
21	CTCF	chr22:31001532-31001881	K562	blood:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
22	MAX	chr22:31001606-31001910	K562	blood:	n/a	n/a
23	RFX5	chr22:31001613-31001891	Hela-S3	cervix:	n/a	n/a
24	CBX3	chr22:31001315-31002046	K562	blood:	n/a	n/a
25	CTCF	chr22:31001680-31001830	NHDF-neo	bronchial:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
26	STAT1	chr22:31001458-31001952	GM12878	blood:	n/a	chr22:31001506-31001513
27	SIN3AK20	chr22:31001555-31001882	A549	lung:	n/a	n/a
28	CTCF	chr22:31001548-31001832	A549	lung:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
29	ELF1	chr22:31001455-31001965	A549	lung:	n/a	n/a
30	BRCA1	chr22:31001681-31002108	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXA1	chr22:31001536-31001919	HepG2	liver:	n/a	n/a
32	GABPA	chr22:31001461-31001912	MCF-7	breast:	n/a	n/a
33	CTCF	chr22:31001680-31001830	HUVEC	blood vessel:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
34	RCOR1	chr22:31001316-31001880	K562	blood:	n/a	n/a
35	MAX	chr22:31001438-31002039	ECC-1	luminal epithelium:	n/a	n/a
36	ZNF143	chr22:31001473-31001977	GM12878	blood:	n/a	n/a
37	RAD21	chr22:31001486-31001930	H1-hESC	embryonic stem cell:	n/a	chr22:31001697-31001711
38	CTCF	chr22:31001067-31002087	SK-N-SH	brain:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
39	RAD21	chr22:31001525-31001864	H1-hESC	embryonic stem cell:	n/a	chr22:31001697-31001711
40	RUNX3	chr22:31001447-31001915	GM12878	blood:	n/a	n/a
41	ELF1	chr22:31001474-31001874	HepG2	liver:	n/a	n/a
42	ZNF143	chr22:31001509-31002045	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr22:31001466-31001982	MCF-7	breast:	n/a	n/a
44	CTCF	chr22:31001680-31001830	NHEK	skin:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
45	CTCF	chr22:31001492-31001916	GM12878	blood:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712
46	TBL1XR1	chr22:31001519-31002117	K562	blood:	n/a	n/a
47	JUND	chr22:31001446-31001927	K562	blood:	n/a	n/a
48	FOXA2	chr22:31001586-31001935	HepG2	liver:	n/a	n/a
49	MAX	chr22:31001597-31001825	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr22:31001595-31001831	Kidney_OC	kidney:	n/a	chr22:31001686-31001695 chr22:31001697-31001710 chr22:31001695-31001713 chr22:31001696-31001712

No.	Distal block	Cell Line	Cell type
1	chr22:31001608..31004689-chr22:31008894..31012791,3	K562	blood:
2	chr22:30840880..30841579-chr22:31001151..31002176,4	MCF-7	breast:
3	chr22:31000969..31001915-chr22:31151437..31152043,2	MCF-7	breast:
4	chr22:30934256..30936381-chr22:31000054..31002763,2	K562	blood:

Variant related genes	Relation type
TCN2	TF binding region
ENSG00000185339	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10418	0.81[CHB][hapmap]
rs11089465	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11703570	0.81[CHB][hapmap]
rs13053923	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs1544468	0.81[CHB][hapmap]
rs2240433	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301955	0.81[CHB][hapmap]
rs2301957	0.81[CHB][hapmap]
rs4820872	0.80[CHB][hapmap]
rs4820876	0.80[CHB][hapmap]
rs4820882	0.82[AMR][1000 genomes]
rs4820888	0.81[CHB][hapmap]
rs5749134	0.81[CHB][hapmap]
rs5749135	0.81[CHB][hapmap]
rs5749148	0.81[CHB][hapmap]
rs5753228	0.86[EUR][1000 genomes]
rs5753229	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5753230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753257	0.81[CHB][hapmap]
rs5753260	0.81[CHB][hapmap]
rs5997694	0.82[ASN][1000 genomes]
rs5997697	0.83[ASN][1000 genomes]
rs5997703	0.81[CHB][hapmap]
rs62227016	0.82[ASN][1000 genomes]
rs737953	0.80[CHB][hapmap]
rs740235	0.81[CHB][hapmap]
rs8138932	0.80[AMR][1000 genomes]
rs9609017	0.92[AMR][1000 genomes]
rs9621047	0.81[CHB][hapmap]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5749131	CRYBB3	cis	parietal	SCAN
rs5749131	DUSP18	cis	lymphoblastoid	seeQTL
rs5749131	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30993200-31002800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:31000800-31002000	Enhancers	Ovary	ovary
3	chr22:31001000-31002800	Enhancers	Stomach Mucosa	stomach
4	chr22:31001200-31002000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr22:31001200-31002000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:31001200-31002000	Enhancers	Colonic Mucosa	Colon
7	chr22:31001200-31002400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr22:31001200-31002400	Enhancers	Pancreas	Pancrea
9	chr22:31001200-31002600	Flanking Active TSS	K562	blood
10	chr22:31001200-31002800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr22:31001400-31002000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:31001400-31002000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr22:31001400-31002000	Enhancers	Liver	Liver
14	chr22:31001400-31002000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr22:31001400-31002000	Enhancers	Fetal Muscle Trunk	muscle
16	chr22:31001400-31002200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr22:31001400-31002200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:31001400-31002200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr22:31001400-31002200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr22:31001400-31002200	Enhancers	Brain Hippocampus Middle	brain
21	chr22:31001400-31002200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:31001400-31002200	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr22:31001400-31002200	Enhancers	Fetal Stomach	stomach
24	chr22:31001400-31002400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr22:31001400-31002400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:31001400-31002400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr22:31001400-31002400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr22:31001400-31002400	Enhancers	Placenta	Placenta
29	chr22:31001400-31002400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr22:31001400-31002400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr22:31001400-31002400	Flanking Active TSS	HUVEC	blood vessel
32	chr22:31001400-31002600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr22:31001400-31002600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr22:31001400-31002600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr22:31001400-31002600	Flanking Active TSS	Osteobl	bone
36	chr22:31001400-31002800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr22:31001400-31002800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr22:31001400-31002800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr22:31001400-31003200	Enhancers	Spleen	Spleen
40	chr22:31001400-31003800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr22:31001400-31006400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr22:31001600-31002000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr22:31001600-31002000	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr22:31001600-31002000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr22:31001600-31002000	Enhancers	Fetal Lung	lung
46	chr22:31001600-31002200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr22:31001600-31002200	Weak transcription	Right Ventricle	heart
48	chr22:31001600-31002200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr22:31001600-31002400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr22:31001600-31002400	Enhancers	Fetal Heart	heart

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