Variant report

Variant	rs3778443
Chromosome Location	chr6:38654488-38654489
allele	A/G
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	POLR2A	chr6:38654487-38654530	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr6:38654041-38654508	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:38606864..38609174-chr6:38653748..38656095,3	K562	blood:
2	chr6:38654394..38655965-chr6:38667989..38670845,2	MCF-7	breast:
3	chr6:38653566..38655174-chr6:38662800..38664328,2	K562	blood:
4	chr6:38652463..38654618-chr6:38669083..38671803,3	K562	blood:

Variant related genes	Relation type
GLO1	TF binding region
ENSG00000124767	Chromatin interaction
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1616723	0.87[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs1626217	0.82[EUR][1000 genomes]
rs16890840	0.85[TSI][hapmap]
rs1781716	0.88[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455773	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2894415	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2894416	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58458015	0.82[EUR][1000 genomes]
rs62396374	0.82[EUR][1000 genomes]
rs62396376	0.82[EUR][1000 genomes]
rs62396379	0.82[EUR][1000 genomes]
rs62396382	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62396384	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62396385	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72855194	0.82[EUR][1000 genomes]
rs9791292	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38614800-38654800	Weak transcription	Brain Angular Gyrus	brain
2	chr6:38641000-38654800	Weak transcription	Fetal Heart	heart
3	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:38641600-38668000	Weak transcription	NHLF	lung
5	chr6:38641800-38654800	Weak transcription	Pancreas	Pancrea
6	chr6:38642000-38657600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:38642200-38656400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:38642400-38654800	Weak transcription	Psoas Muscle	Psoas
9	chr6:38642400-38655200	Strong transcription	NHEK	skin
10	chr6:38642400-38657000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:38642400-38660000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:38642400-38665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:38642600-38654600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:38642600-38655000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:38642600-38655200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:38642800-38655600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:38642800-38658000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:38643200-38656200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:38645000-38656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:38646000-38670000	Weak transcription	A549	lung
22	chr6:38646600-38656400	Weak transcription	Colonic Mucosa	Colon
23	chr6:38646600-38656400	Weak transcription	Spleen	Spleen
24	chr6:38646600-38663400	Weak transcription	Esophagus	oesophagus
25	chr6:38646800-38654800	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:38646800-38655000	Weak transcription	Aorta	Aorta
27	chr6:38646800-38656400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:38646800-38656400	Weak transcription	Fetal Brain Female	brain
29	chr6:38646800-38656400	Weak transcription	Gastric	stomach
30	chr6:38646800-38668200	Weak transcription	Primary T cells from cord blood	blood
31	chr6:38647000-38656200	Weak transcription	Brain Germinal Matrix	brain
32	chr6:38647200-38657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:38647200-38659000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:38647400-38654800	Weak transcription	Right Ventricle	heart
35	chr6:38647400-38655200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:38647400-38656000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:38647400-38656400	Weak transcription	Thymus	Thymus
38	chr6:38647800-38655600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:38648200-38655000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:38648800-38669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:38649200-38655400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:38649200-38656400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:38649400-38654600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:38649800-38655000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:38650200-38656200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:38650200-38656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:38650200-38656400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:38650200-38663400	Weak transcription	HUVEC	blood vessel
49	chr6:38650200-38666600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:38650800-38654800	Weak transcription	Small Intestine	intestine

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