Variant report

Variant	rs6537798
Chromosome Location	chr1:114351706-114351707
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:114351424-114351879	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:114351498-114351744	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:114351322-114351787	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:114351502-114351768	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:114351466-114351797	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:114351454-114351787	MCF10A-Er-Src	breast:	n/a	n/a
7	TBL1XR1	chr1:114351576-114351893	K562	blood:	n/a	n/a
8	STAT3	chr1:114351537-114351727	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
2	chr1:114350122..114352363-chr1:114460865..114462915,2	MCF-7	breast:
3	chr1:114299192..114304079-chr1:114351100..114353758,4	K562	blood:
4	chr1:108135408..108137327-chr1:114351210..114352891,3	MCF-7	breast:
5	chr1:114349816..114352777-chr1:115298832..115300694,3	MCF-7	breast:
6	chr1:114300710..114302540-chr1:114351249..114353221,2	K562	blood:
7	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231128	TF binding region
ENSG00000009307	Chromatin interaction
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10858016	0.85[ASN][1000 genomes]
rs11102678	0.87[ASW][hapmap]
rs1111695	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs1217375	0.87[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs1217378	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217379	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217385	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217404	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1217405	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217408	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs1217409	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217411	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217418	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217420	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1230682	0.96[ASN][1000 genomes]
rs1230686	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1235005	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1310182	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539437	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1624335	0.81[ASW][hapmap]
rs1743594	0.81[ASW][hapmap]
rs1935836	0.87[YRI][hapmap]
rs1970559	0.88[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs2185971	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2273758	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2476599	0.87[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs2476600	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476602	0.87[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs2476604	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797414	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.96[ASN][1000 genomes]
rs2797416	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789598	0.81[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4991898	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665194	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672018	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7555634	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556622	0.85[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6537798	PHTF1	cis	cerebellum	SCAN
rs6537798	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:114332400-114353400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:114337200-114352600	Weak transcription	Fetal Kidney	kidney
8	chr1:114340000-114351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:114340400-114352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:114340600-114351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:114340600-114351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:114340600-114351800	Weak transcription	Thymus	Thymus
13	chr1:114340600-114353400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:114340800-114352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:114340800-114352800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:114342000-114352600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:114342200-114351800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:114344400-114351800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:114345800-114351800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:114346800-114352400	Weak transcription	Colonic Mucosa	Colon
21	chr1:114347000-114352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:114347200-114352000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:114347200-114352000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:114347200-114352400	Weak transcription	Ovary	ovary
25	chr1:114347400-114351800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:114347400-114352400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:114347400-114352600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:114347400-114352600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:114347600-114351800	Weak transcription	Fetal Lung	lung
30	chr1:114347800-114351800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:114348000-114351800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:114348000-114351800	Weak transcription	Psoas Muscle	Psoas
33	chr1:114348000-114351800	Weak transcription	NH-A	brain
34	chr1:114348000-114351800	Weak transcription	NHLF	lung
35	chr1:114348000-114352000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:114348000-114352600	Weak transcription	HSMM	muscle
37	chr1:114348200-114351800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:114348200-114353600	Weak transcription	Placenta	Placenta
39	chr1:114348600-114351800	Weak transcription	Right Atrium	heart
40	chr1:114348600-114351800	Weak transcription	A549	lung
41	chr1:114348600-114352400	Weak transcription	Fetal Thymus	thymus
42	chr1:114348600-114352600	Weak transcription	Small Intestine	intestine
43	chr1:114348600-114353800	Weak transcription	Gastric	stomach
44	chr1:114349200-114352400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:114349600-114352400	Weak transcription	Spleen	Spleen
46	chr1:114349800-114352600	Weak transcription	Left Ventricle	heart
47	chr1:114349800-114353600	Weak transcription	Lung	lung
48	chr1:114350000-114352600	Weak transcription	Fetal Stomach	stomach
49	chr1:114350200-114351800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:114350400-114351800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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