Variant report

Variant	rs6661903
Chromosome Location	chr1:171457707-171457708
allele	A/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	GATA1	chr1:171457442-171458107	PBDE	blood:	n/a	chr1:171457894-171457906
2	EP300	chr1:171457565-171458151	T-47D	breast:	n/a	n/a
3	GATA3	chr1:171457331-171458139	T-47D	breast:	n/a	chr1:171457894-171457906 chr1:171457895-171457903
4	GATA3	chr1:171457630-171458077	T-47D	breast:	n/a	chr1:171457894-171457906 chr1:171457895-171457903
5	FOXA1	chr1:171457675-171457931	T-47D	breast:	n/a	n/a
6	GATA2	chr1:171457619-171458162	HUVEC	blood vessel:	n/a	chr1:171457894-171457906
7	GATA3	chr1:171457639-171458092	MCF-7	breast:	n/a	chr1:171457894-171457906 chr1:171457895-171457903

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171452969..171454844-chr1:171456792..171458676,3	K562	blood:
2	chr1:171454829..171458429-chr1:171468344..171472224,4	MCF-7	breast:

Variant related genes	Relation type
RN7SL425P	TF binding region
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10737319	0.91[AMR][1000 genomes]
rs10798424	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798429	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1980512	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2207191	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235511	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916386	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4916395	0.91[AMR][1000 genomes]
rs6701071	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7543159	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171453600-171458200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:171454000-171457800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171455600-171458000	Flanking Active TSS	HUVEC	blood vessel
4	chr1:171455600-171458200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr1:171455600-171461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:171455800-171459000	Enhancers	Stomach Mucosa	stomach
7	chr1:171455800-171461600	Weak transcription	Gastric	stomach
8	chr1:171455800-171465400	Weak transcription	Lung	lung
9	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
10	chr1:171456000-171459000	Weak transcription	Pancreas	Pancrea
11	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
12	chr1:171456200-171457800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:171456200-171457800	Enhancers	Rectal Smooth Muscle	rectum
14	chr1:171456200-171458000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:171456200-171458000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr1:171456200-171458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:171456200-171458000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:171456200-171459800	Enhancers	Fetal Heart	heart
19	chr1:171456200-171461600	Weak transcription	Left Ventricle	heart
20	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:171456400-171457800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:171456400-171457800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:171456400-171458000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:171456400-171458000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:171456400-171458000	Enhancers	Osteobl	bone
27	chr1:171456400-171458200	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:171456400-171458400	Enhancers	Brain Hippocampus Middle	brain
29	chr1:171456400-171458400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:171456400-171459000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:171456400-171460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:171456400-171460200	Enhancers	Liver	Liver
33	chr1:171456400-171460600	Enhancers	Colon Smooth Muscle	Colon
34	chr1:171456400-171461600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:171456400-171462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:171456400-171462400	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:171456400-171466000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:171456400-171467200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:171456400-171467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:171456400-171468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:171456400-171470200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
43	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
46	chr1:171456600-171458200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:171456600-171458200	Enhancers	Fetal Brain Female	brain
48	chr1:171456600-171458400	Enhancers	Brain Anterior Caudate	brain
49	chr1:171456600-171459000	Genic enhancers	Hela-S3	cervix
50	chr1:171456600-171460200	Weak transcription	H1 Cell Line	embryonic stem cell

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