Variant report

Variant	rs6681666
Chromosome Location	chr1:226189591-226189592
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	STAT3	chr1:226189400-226190335	MCF10A-Er-Src	breast:	n/a	chr1:226190140-226190161 chr1:226190026-226190034 chr1:226189663-226189671
2	ZNF143	chr1:226189419-226190967	K562	blood:	n/a	n/a
3	MTA3	chr1:226189542-226190847	GM12878	blood:	n/a	n/a
4	JUN	chr1:226188614-226191131	K562	blood:	n/a	chr1:226190415-226190427 chr1:226189662-226189671 chr1:226189874-226189883
5	EP300	chr1:226189494-226191225	K562	blood:	n/a	chr1:226189588-226189602
6	POLR2A	chr1:226189557-226191009	H1-neurons	neurons:	n/a	n/a
7	CREB1	chr1:226189587-226190494	GM12878	blood:	n/a	chr1:226189872-226189885
8	EP300	chr1:226189563-226191103	GM12878	blood:	n/a	chr1:226189588-226189602
9	GABPA	chr1:226189533-226190542	HL-60	blood:	n/a	n/a
10	ZNF384	chr1:226189587-226191076	K562	blood:	n/a	n/a
11	TEAD4	chr1:226189392-226191116	K562	blood:	n/a	n/a
12	RFX5	chr1:226189580-226190303	K562	blood:	n/a	n/a
13	KAP1	chr1:226189503-226190898	U2OS	brain:	n/a	n/a
14	REST	chr1:226189445-226191304	H1-neurons	neurons:	n/a	chr1:226190577-226190590
15	NR2F2	chr1:226189531-226191682	K562	blood:	n/a	n/a
16	SPI1	chr1:226189526-226190545	GM12878	blood:	n/a	chr1:226189944-226189957
17	BHLHE40	chr1:226189570-226190447	GM12878	blood:	n/a	n/a
18	CREB1	chr1:226189537-226190448	GM12878	blood:	n/a	chr1:226189872-226189885
19	TBL1XR1	chr1:226189423-226191594	K562	blood:	n/a	n/a
20	CBX3	chr1:226189586-226191105	K562	blood:	n/a	n/a
21	ZNF384	chr1:226189562-226190187	GM12878	blood:	n/a	n/a
22	CEBPB	chr1:226189518-226191088	K562	blood:	n/a	chr1:226189590-226189603

No.	Distal block	Cell Line	Cell type
1	chr1:226148548..226150301-chr1:226188144..226190996,2	K562	blood:
2	chr1:226188590..226191989-chr1:226218669..226223499,6	K562	blood:
3	chr1:225614620..225617599-chr1:226187708..226190219,2	K562	blood:
4	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
5	chr1:226187874..226190820-chr1:226213394..226216312,2	K562	blood:
6	chr1:226110464..226115809-chr1:226185735..226190763,7	K562	blood:
7	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
8	chr1:226188843..226191078-chr1:226237826..226239830,2	K562	blood:
9	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
10	chr1:226188139..226192155-chr1:226228386..226234051,6	K562	blood:
11	chr1:226147735..226150048-chr1:226187163..226189644,2	K562	blood:
12	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:
13	chr1:226187840..226190663-chr1:226296821..226299236,2	MCF-7	breast:
14	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
15	chr1:226185796..226188880-chr1:226188906..226190706,6	MCF-7	breast:
16	chr1:225614459..225616811-chr1:226187382..226190190,2	K562	blood:

Variant related genes	Relation type
SDE2	TF binding region
ENSG00000143811	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11586667	0.86[JPT][hapmap]
rs11590226	0.86[JPT][hapmap]
rs11808474	0.86[JPT][hapmap]
rs16845468	0.86[JPT][hapmap]
rs3795442	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73100519	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100530	1.00[ASN][1000 genomes]
rs7554619	0.86[JPT][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	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226187400-226191000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:226187600-226189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:226187600-226189800	Weak transcription	Gastric	stomach
4	chr1:226187600-226189800	Weak transcription	Spleen	Spleen
5	chr1:226187800-226189600	Weak transcription	NHDF-Ad	bronchial
6	chr1:226187800-226189800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:226187800-226189800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:226187800-226189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:226187800-226189800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:226187800-226189800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:226187800-226189800	Weak transcription	Esophagus	oesophagus
12	chr1:226187800-226189800	Weak transcription	Pancreas	Pancrea
13	chr1:226187800-226189800	Weak transcription	Right Ventricle	heart
14	chr1:226187800-226189800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:226187800-226189800	Weak transcription	HMEC	breast
16	chr1:226187800-226190000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:226187800-226190000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:226187800-226190000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:226187800-226190000	Weak transcription	Left Ventricle	heart
20	chr1:226187800-226190000	Weak transcription	NHLF	lung
21	chr1:226187800-226190200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:226187800-226190200	Weak transcription	Liver	Liver
23	chr1:226187800-226190400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:226187800-226190400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:226187800-226191000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:226188000-226189600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:226188000-226189800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:226188000-226189800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:226188000-226189800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:226188000-226189800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:226188000-226189800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:226188000-226189800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:226188000-226189800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:226188000-226189800	Weak transcription	Brain Substantia Nigra	brain
35	chr1:226188000-226189800	Weak transcription	HSMM	muscle
36	chr1:226188000-226189800	Weak transcription	HSMMtube	muscle
37	chr1:226188000-226189800	Weak transcription	NHEK	skin
38	chr1:226188000-226190000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:226188000-226190000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:226188000-226190000	Enhancers	Brain Anterior Caudate	brain
41	chr1:226188000-226190000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:226188000-226190800	Enhancers	Stomach Mucosa	stomach
43	chr1:226188000-226198600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:226188200-226189600	Weak transcription	Hela-S3	cervix
45	chr1:226188200-226189800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:226188200-226189800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:226188200-226189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:226188200-226189800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:226188200-226189800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:226188200-226189800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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