Variant report

Variant	rs421328
Chromosome Location	chr6:33401872-33401873
allele	C/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	chr6:33401547-33401892	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP4	chr6:33401540-33401928	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:33401223-33401886	H1-hESC	embryonic stem cell:	n/a	n/a
4	CREB1	chr6:33401377-33401922	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr6:33400773-33401900	H1-hESC	embryonic stem cell:	n/a	chr6:33400888-33400896
6	MAZ	chr6:33401096-33401954	IMR90	lung:	n/a	n/a
7	TEAD4	chr6:33401496-33401903	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33395899..33401993-chr6:33420102..33423796,11	MCF-7	breast:
2	chr6:33398677..33403495-chr6:33419995..33423723,6	K562	blood:
3	chr6:33399707..33401893-chr6:33408144..33410005,2	MCF-7	breast:

Variant related genes	Relation type
SYNGAP1	TF binding region
MIR5004	TF binding region
ENSG00000213588	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1755040	0.84[AMR][1000 genomes]
rs210131	0.81[EUR][1000 genomes]
rs210190	0.88[AMR][1000 genomes]
rs2747476	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28800551	0.88[AMR][1000 genomes]
rs3119019	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119021	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119022	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3119024	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3119025	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119026	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3119027	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130023	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130024	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130026	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130032	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130035	0.85[EUR][1000 genomes]
rs34416888	0.80[AMR][1000 genomes]
rs35432298	0.88[AMR][1000 genomes]
rs35700288	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35796955	0.88[AMR][1000 genomes]
rs35817932	0.88[AMR][1000 genomes]
rs36003672	0.88[AMR][1000 genomes]
rs406009	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs413722	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449978	0.84[AMR][1000 genomes]
rs4713634	0.81[EUR][1000 genomes]
rs498066	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761582	1.00[AFR][1000 genomes];0.96[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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1019212	chr6:33398031-33413930	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	16 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	chr6:33396400-33403000	Weak transcription	Ovary	ovary
2	chr6:33396400-33405200	Weak transcription	Psoas Muscle	Psoas
3	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
4	chr6:33396800-33402000	Enhancers	Fetal Lung	lung
5	chr6:33396800-33403000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:33396800-33403000	Weak transcription	Aorta	Aorta
7	chr6:33398400-33402000	Enhancers	Right Ventricle	heart
8	chr6:33398600-33402200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:33398600-33403000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:33398600-33403000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:33398800-33403000	Weak transcription	Osteobl	bone
12	chr6:33399200-33403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:33399200-33403400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:33399200-33403600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:33399400-33402200	Enhancers	Colon Smooth Muscle	Colon
16	chr6:33399400-33402200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:33399400-33402200	Enhancers	Rectal Smooth Muscle	rectum
18	chr6:33399400-33402800	Weak transcription	Esophagus	oesophagus
19	chr6:33399400-33403000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:33399400-33403000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:33399400-33403000	Weak transcription	Adipose Nuclei	Adipose
22	chr6:33399400-33403400	Weak transcription	NHEK	skin
23	chr6:33399400-33421200	Weak transcription	HMEC	breast
24	chr6:33399400-33421600	Weak transcription	Stomach Mucosa	stomach
25	chr6:33399600-33402600	Genic enhancers	Fetal Stomach	stomach
26	chr6:33399600-33403000	Weak transcription	Brain Substantia Nigra	brain
27	chr6:33399600-33403000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:33399600-33403200	Weak transcription	Liver	Liver
29	chr6:33399600-33403600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:33399600-33409200	Weak transcription	Small Intestine	intestine
31	chr6:33399600-33421400	Weak transcription	HUVEC	blood vessel
32	chr6:33399800-33403000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:33399800-33421400	Weak transcription	A549	lung
34	chr6:33400000-33402000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:33400000-33402200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr6:33400000-33403200	Weak transcription	Colonic Mucosa	Colon
37	chr6:33400000-33412800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:33400000-33418000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:33400000-33420600	Strong transcription	Brain Germinal Matrix	brain
40	chr6:33400200-33402200	Enhancers	NH-A	brain
41	chr6:33400200-33402600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:33400200-33403000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:33400200-33403000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:33400200-33403000	Weak transcription	Placenta	Placenta
45	chr6:33400200-33403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:33400400-33402000	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:33400400-33402000	Genic enhancers	NHLF	lung
48	chr6:33400400-33402200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:33400400-33406000	Weak transcription	Fetal Brain Male	brain
50	chr6:33400600-33402200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links