Variant report

Variant	rs4951583
Chromosome Location	chr1:212416078-212416079
allele	C/T
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	RCOR1	chr1:212415022-212416386	K562	blood:	n/a	n/a
2	HCFC1	chr1:212415497-212416434	K562	blood:	n/a	n/a
3	JUND	chr1:212415132-212416213	K562	blood:	n/a	chr1:212415926-212415938
4	IRF1	chr1:212415433-212416155	K562	blood:	n/a	chr1:212415851-212415861 chr1:212415851-212415865
5	CBX3	chr1:212414891-212416492	K562	blood:	n/a	n/a
6	JUND	chr1:212415932-212416275	HepG2	liver:	n/a	n/a
7	HEY1	chr1:212415522-212416410	HepG2	liver:	n/a	n/a
8	EP300	chr1:212415611-212416361	HepG2	liver:	n/a	chr1:212415929-212415943
9	TEAD4	chr1:212415743-212416276	HepG2	liver:	n/a	n/a
10	FOXA1	chr1:212415637-212416345	HepG2	liver:	n/a	n/a
11	ZBTB7A	chr1:212415891-212416296	HepG2	liver:	n/a	n/a
12	NFIC	chr1:212415671-212416231	HepG2	liver:	n/a	n/a
13	ZMIZ1	chr1:212415568-212416487	K562	blood:	n/a	n/a
14	RXRA	chr1:212415844-212416295	HepG2	liver:	n/a	n/a
15	ELF1	chr1:212415333-212416348	K562	blood:	n/a	chr1:212415732-212415743 chr1:212415732-212415743
16	EP300	chr1:212415514-212416321	HepG2	liver:	n/a	chr1:212415929-212415943
17	BHLHE40	chr1:212415556-212416629	K562	blood:	n/a	n/a
18	FOXA1	chr1:212415711-212416250	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:212416054-212416083	HepG2	liver:	n/a	n/a
20	NR2F2	chr1:212415571-212416198	K562	blood:	n/a	n/a
21	FOXA1	chr1:212415688-212416269	HepG2	liver:	n/a	n/a
22	TAL1	chr1:212415583-212416095	K562	blood:	n/a	n/a
23	ELF1	chr1:212415526-212416325	HepG2	liver:	n/a	chr1:212415732-212415743 chr1:212415732-212415743
24	IRF1	chr1:212415508-212416192	K562	blood:	n/a	chr1:212415851-212415861 chr1:212415851-212415865
25	EP300	chr1:212415558-212416341	K562	blood:	n/a	chr1:212415929-212415943
26	GATA2	chr1:212415534-212416084	HUVEC	blood vessel:	n/a	n/a
27	MAX	chr1:212415554-212416198	K562	blood:	n/a	n/a
28	MAFK	chr1:212414888-212416291	K562	blood:	n/a	chr1:212415220-212415235 chr1:212415341-212415352
29	ZNF384	chr1:212415379-212416085	K562	blood:	n/a	n/a
30	TCF7L2	chr1:212415747-212416402	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:212415523-212416193	K562	blood:	n/a	n/a
32	TBP	chr1:212415561-212416102	K562	blood:	n/a	n/a
33	NR2F2	chr1:212414857-212416772	K562	blood:	n/a	chr1:212414878-212414893
34	MYC	chr1:212415584-212416518	K562	blood:	n/a	n/a
35	MXI1	chr1:212415822-212416242	HepG2	liver:	n/a	n/a
36	FOXA2	chr1:212415612-212416254	HepG2	liver:	n/a	n/a
37	TBP	chr1:212415619-212416349	HepG2	liver:	n/a	n/a
38	MAFK	chr1:212415666-212416080	HepG2	liver:	n/a	n/a
39	TBL1XR1	chr1:212414889-212416081	K562	blood:	n/a	n/a
40	UBTF	chr1:212415488-212416152	K562	blood:	n/a	n/a
41	ELF1	chr1:212415501-212416247	K562	blood:	n/a	chr1:212415732-212415743 chr1:212415732-212415743
42	ZBTB7A	chr1:212416058-212416318	HepG2	liver:	n/a	n/a
43	HMGN3	chr1:212415615-212416386	K562	blood:	n/a	n/a
44	POLR2A	chr1:212415602-212416384	HepG2	liver:	n/a	n/a
45	FOXA1	chr1:212415784-212416280	HepG2	liver:	n/a	n/a
46	MAX	chr1:212415996-212416286	HepG2	liver:	n/a	n/a
47	ELF1	chr1:212415470-212416352	HepG2	liver:	n/a	chr1:212415732-212415743 chr1:212415732-212415743
48	MAZ	chr1:212415349-212416295	K562	blood:	n/a	n/a
49	MYBL2	chr1:212415513-212416390	HepG2	liver:	n/a	n/a
50	HEY1	chr1:212415479-212416138	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212413989..212416642-chr1:212457205..212458849,2	K562	blood:
2	chr1:212413271..212416807-chr1:212458908..212461742,4	K562	blood:
3	chr1:212385419..212387445-chr1:212414285..212417488,3	K562	blood:
4	chr1:212414204..212417772-chr1:212418799..212421886,6	K562	blood:

Variant related genes	Relation type
ENSG00000226251	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1565737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168438	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492746	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351374	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351376	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351385	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351386	0.88[GIH][hapmap]
rs351387	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs351388	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351408	0.85[GIH][hapmap]
rs4951441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4951583	KCNH1	cis	cerebellum	SCAN
rs4951583	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs4951583	TMEM206	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:212408600-212416200	Weak transcription	Fetal Stomach	stomach
3	chr1:212410200-212417000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:212410600-212416200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:212412200-212417400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:212412200-212417400	Weak transcription	GM12878-XiMat	blood
7	chr1:212412400-212417800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:212412400-212420600	Weak transcription	Fetal Lung	lung
9	chr1:212412800-212416200	Weak transcription	Lung	lung
10	chr1:212413000-212416200	Weak transcription	Esophagus	oesophagus
11	chr1:212413200-212420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:212414600-212416600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:212414800-212416400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:212414800-212416400	Flanking Active TSS	HepG2	liver
15	chr1:212414800-212416600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:212414800-212416800	Enhancers	Liver	Liver
17	chr1:212415000-212416200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:212415000-212416600	Flanking Active TSS	K562	blood
19	chr1:212415200-212416600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:212415200-212419800	Weak transcription	Spleen	Spleen
21	chr1:212415200-212420400	Weak transcription	Fetal Heart	heart
22	chr1:212415200-212420800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:212415400-212416400	Enhancers	Brain Angular Gyrus	brain
24	chr1:212415400-212416600	Enhancers	Fetal Intestine Large	intestine
25	chr1:212415400-212417200	Enhancers	Stomach Mucosa	stomach
26	chr1:212415600-212416400	Enhancers	Brain Hippocampus Middle	brain
27	chr1:212415600-212416400	Enhancers	Colonic Mucosa	Colon
28	chr1:212415600-212416400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:212415600-212416600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:212415600-212416600	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr1:212415600-212416800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr1:212415800-212416200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr1:212415800-212416400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:212416000-212416200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:212416000-212416200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:212416000-212416200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr1:212416000-212416200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr1:212416000-212416400	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr1:212416000-212416400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:212416000-212416400	Enhancers	Psoas Muscle	Psoas
41	chr1:212416000-212416400	Enhancers	HUVEC	blood vessel
42	chr1:212416000-212416600	Enhancers	Brain Anterior Caudate	brain
43	chr1:212416000-212416600	Enhancers	Brain Substantia Nigra	brain
44	chr1:212416000-212416600	Enhancers	Left Ventricle	heart
45	chr1:212416000-212416600	Enhancers	Right Atrium	heart
46	chr1:212416000-212416600	Enhancers	Right Ventricle	heart
47	chr1:212416000-212416800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr1:212416000-212417400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:212416000-212418200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:212416000-212420600	Weak transcription	Osteobl	bone

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