Variant report

Variant	rs2413049
Chromosome Location	chr22:31686144-31686145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31685486-31688678	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr22:31686104-31687229	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr22:31685512-31686296	GM12892	blood:	n/a	n/a
4	RFX5	chr22:31686144-31689109	SK-N-SH	brain:	n/a	chr22:31686823-31686832
5	POLR2A	chr22:31685792-31687156	GM12891	blood:	n/a	n/a
6	CEBPB	chr22:31686119-31687000	Hela-S3	cervix:	n/a	n/a
7	MYC	chr22:31686125-31687192	NB4	blood:	n/a	n/a
8	POLR2A	chr22:31685884-31687164	GM18526	blood:	n/a	n/a
9	JUN	chr22:31685703-31687295	K562	blood:	n/a	chr22:31686824-31686833
10	POLR2A	chr22:31685974-31687359	GM12892	blood:	n/a	n/a
11	ELF1	chr22:31685981-31687433	GM12878	blood:	n/a	chr22:31686300-31686313 chr22:31686774-31686783 chr22:31686837-31686846 chr22:31686849-31686861 chr22:31687398-31687410
12	POLR2A	chr22:31685962-31687330	K562	blood:	n/a	n/a
13	POLR2A	chr22:31685754-31686232	GM12892	blood:	n/a	n/a
14	POLR2A	chr22:31685377-31687778	GM18505	blood:	n/a	n/a
15	BHLHE40	chr22:31686118-31688719	K562	blood:	n/a	chr22:31686908-31686924
16	ELF1	chr22:31686069-31686546	K562	blood:	n/a	chr22:31686300-31686313

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:31686097-31686147	AG09309	skin:	n/a
2	chr22:31686097-31686147	GM06990	blood:	n/a
3	chr22:31686097-31686147	K562	blood:	n/a
4	chr22:31686097-31686147	HPAEpiC	pulmonary alveolar:	n/a
5	chr22:31686097-31686147	LNCaP	prostate:	n/a
6	chr22:31686097-31686147	AG04450	lung:	fetal
7	chr22:31686097-31686147	HUVEC	blood vessel:	n/a
8	chr22:31686097-31686147	GM12892	blood:	n/a
9	chr22:31686097-31686147	BJ	skin:	n/a
10	chr22:31686097-31686147	MCF10A-Er-Src	breast:	n/a
11	chr22:31686097-31686147	PrEC	prostate:	n/a
12	chr22:31686097-31686147	NHDF-neo	bronchial:	n/a
13	chr22:31686097-31686147	HCT-116	colon:	n/a
14	chr22:31686097-31686147	NB4	blood:	n/a
15	chr22:31686097-31686147	A549	lung:	n/a
16	chr22:31686097-31686147	HNPCEpiC	eye:	n/a
17	chr22:31686097-31686147	ECC-1	luminal epithelium:	n/a
18	chr22:31686097-31686147	U87	brain:	n/a
19	chr22:31686097-31686147	MCF-7	breast:	n/a
20	chr22:31686097-31686147	ovcar-3	ovarian:	n/a
21	chr22:31686097-31686147	PFSK-1	brain:	n/a
22	chr22:31686097-31686147	HMEC	breast:	n/a
23	chr22:31686097-31686147	SAEC	small airway:	n/a
24	chr22:31686097-31686147	PANC-1	pancreas:	n/a
25	chr22:31686097-31686147	ProgFib	skin:	n/a
26	chr22:31686097-31686147	GM12878	blood:	n/a
27	chr22:31686097-31686147	SKMC	muscle:	n/a
28	chr22:31686097-31686147	HRCEpiC	kidney:	n/a
29	chr22:31686097-31686147	HepG2	liver:	n/a
30	chr22:31686097-31686147	HCF	heart:	n/a
31	chr22:31686097-31686147	Caco-2	colon:	n/a
32	chr22:31686097-31686147	HRE	kidney:	n/a
33	chr22:31686097-31686147	GM12891	blood:	n/a
34	chr22:31686097-31686147	SK-N-MC	brain:	n/a
35	chr22:31686097-31686147	AoSMC	blood vessel:	n/a
36	chr22:31686097-31686147	HCM	heart:	n/a
37	chr22:31686097-31686147	HL-60	blood:	n/a
38	chr22:31686097-31686147	CMK	blood:	n/a
39	chr22:31686097-31686147	HRPEpiC	eye:	n/a
40	chr22:31686097-31686147	SK-N-SH	brain:	n/a
41	chr22:31686097-31686147	Hela-S3	cervix:	n/a
42	chr22:31686097-31686147	T-47D	breast:	n/a
43	chr22:31686097-31686147	HIPEpiC	eye:	n/a
44	chr22:31686097-31686147	AG04449	skin:	fetal
45	chr22:31686097-31686147	AG10803	skin:	n/a
46	chr22:31686097-31686147	NHBE	bronchial:	n/a
47	chr22:31686097-31686147	GM19239	blood:	n/a
48	chr22:31686097-31686147	NH-A	brain:	n/a
49	chr22:31686097-31686147	HEK293	kidney:	embryo
50	chr22:31686097-31686147	Jurkat	blood:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
2	chr22:31659364..31661721-chr22:31683872..31686646,3	MCF-7	breast:
3	chr22:31686029..31689751-chr22:31793811..31797004,3	K562	blood:
4	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
5	chr22:31679718..31681431-chr22:31684803..31686641,2	K562	blood:
6	chr22:31685604..31688964-chr22:31794244..31796594,4	MCF-7	breast:
7	chr22:31683610..31686152-chr22:31686912..31689729,2	MCF-7	breast:
8	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:
9	chr22:31642936..31645707-chr22:31684888..31688055,3	MCF-7	breast:
10	chr22:31684558..31686657-chr22:31740463..31743342,2	K562	blood:
11	chr22:31682441..31684194-chr22:31684357..31686395,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228839	TF binding region
ENSG00000228839	CpG island
ENSG00000213888	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000228839	Chromatin interaction
ENSG00000185721	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1034588	0.91[EUR][1000 genomes]
rs1034589	0.85[EUR][1000 genomes]
rs12152166	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13054220	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs131205	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858821	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2040533	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073857	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2078803	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2079431	0.85[EUR][1000 genomes]
rs2106294	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2228619	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283879	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2283881	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2413032	0.82[EUR][1000 genomes]
rs2413033	0.85[EUR][1000 genomes]
rs2413034	0.86[EUR][1000 genomes]
rs2413035	0.90[EUR][1000 genomes]
rs2413046	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413047	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141404	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299418	0.89[EUR][1000 genomes]
rs4603880	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4820042	0.90[EUR][1000 genomes]
rs4820043	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820951	0.90[EUR][1000 genomes]
rs4820962	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4820963	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749224	0.85[EUR][1000 genomes]
rs5749229	0.90[EUR][1000 genomes]
rs5749243	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753500	0.85[EUR][1000 genomes]
rs5753507	0.84[EUR][1000 genomes]
rs5753521	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753543	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59315359	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997902	0.88[EUR][1000 genomes]
rs5997912	0.90[EUR][1000 genomes]
rs5997913	0.86[EUR][1000 genomes]
rs5997933	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997939	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997949	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71324184	0.84[EUR][1000 genomes]
rs714909	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs715510	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7287267	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737684	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737887	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737888	0.91[EUR][1000 genomes]
rs8135344	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135347	0.87[EUR][1000 genomes]
rs8138596	0.84[EUR][1000 genomes]
rs9606830	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9606831	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609254	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609257	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609264	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609265	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609266	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609267	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9609268	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9621235	0.89[AMR][1000 genomes];0.89[EUR][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	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413049	SFI1	cis	Thyroid	GTEx
rs2413049	DRG1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
3	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
4	chr22:31675400-31686400	Weak transcription	NH-A	brain
5	chr22:31678000-31686400	Weak transcription	HMEC	breast
6	chr22:31679200-31686400	Weak transcription	HSMM	muscle
7	chr22:31679200-31686600	Weak transcription	Ovary	ovary
8	chr22:31679400-31686400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr22:31680400-31688400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
10	chr22:31680600-31687200	Transcr. at gene 5' and 3'	Thymus	Thymus
11	chr22:31681000-31686600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr22:31681200-31686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:31681200-31686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:31681200-31686400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:31682600-31687400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
16	chr22:31683000-31686200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr22:31683200-31686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:31683200-31688200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
19	chr22:31683600-31686600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
20	chr22:31684000-31686600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
21	chr22:31684200-31686400	Weak transcription	Aorta	Aorta
22	chr22:31684600-31686200	Genic enhancers	Fetal Intestine Large	intestine
23	chr22:31684600-31686400	Enhancers	HepG2	liver
24	chr22:31684800-31686200	Genic enhancers	Fetal Intestine Small	intestine
25	chr22:31684800-31686200	Flanking Active TSS	GM12878-XiMat	blood
26	chr22:31685000-31686200	Genic enhancers	Fetal Lung	lung
27	chr22:31685000-31686400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr22:31685000-31686600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr22:31685000-31687200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:31685200-31686200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr22:31685200-31686200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr22:31685200-31686200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
33	chr22:31685200-31686200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
34	chr22:31685200-31686200	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
35	chr22:31685200-31686400	Enhancers	Primary hematopoietic stem cells	blood
36	chr22:31685400-31686200	Flanking Active TSS	Hela-S3	cervix
37	chr22:31685400-31686400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:31685400-31686400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr22:31685600-31686200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr22:31685600-31686200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:31685600-31686200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr22:31685600-31686200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr22:31685600-31686200	Enhancers	Fetal Muscle Leg	muscle
44	chr22:31685600-31686200	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr22:31685600-31686200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr22:31685600-31686400	Enhancers	Left Ventricle	heart
47	chr22:31685600-31686400	Weak transcription	Osteobl	bone
48	chr22:31685600-31686600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr22:31685600-31686600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
50	chr22:31685600-31686600	Enhancers	Fetal Brain Male	brain

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