Variant report

Variant	rs13212809
Chromosome Location	chr6:74360511-74360512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74356240..74358811-chr6:74359170..74360800,2	MCF-7	breast:
2	chr6:74355210..74358069-chr6:74359193..74361548,3	K562	blood:
3	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
4	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
5	chr6:74228067..74234767-chr6:74357105..74365312,16	MCF-7	breast:
6	chr6:74347373..74350038-chr6:74360167..74362055,2	K562	blood:

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10455281	0.94[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498892	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10943112	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943113	0.93[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943117	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964414	0.86[ASN][1000 genomes]
rs12189556	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193002	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195068	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195584	0.86[ASN][1000 genomes]
rs12196281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197318	0.86[ASN][1000 genomes]
rs12197927	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12203363	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210126	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210394	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210825	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211279	1.00[ASN][1000 genomes]
rs12212297	0.86[ASN][1000 genomes]
rs12213067	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213868	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214877	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216092	1.00[ASN][1000 genomes]
rs13193629	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202151	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203297	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13207999	1.00[ASN][1000 genomes]
rs13211453	1.00[ASN][1000 genomes]
rs2351118	1.00[ASN][1000 genomes]
rs2351119	1.00[ASN][1000 genomes]
rs2351120	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2351121	1.00[ASN][1000 genomes]
rs34342150	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34613232	1.00[ASN][1000 genomes]
rs35256309	0.86[ASN][1000 genomes]
rs35468063	1.00[ASN][1000 genomes]
rs35584640	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35659919	0.86[ASN][1000 genomes]
rs35733187	1.00[ASN][1000 genomes]
rs36131846	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734518	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3757109	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757111	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799288	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708065	1.00[ASN][1000 genomes]
rs56086551	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59383274	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438456	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72949387	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744053	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784805	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS 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 lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74297000-74361800	Weak transcription	GM12878-XiMat	blood
2	chr6:74307200-74362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:74314200-74362800	Weak transcription	Stomach Mucosa	stomach
4	chr6:74315600-74362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:74324600-74362800	Weak transcription	Pancreas	Pancrea
6	chr6:74324800-74361600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:74325400-74362800	Weak transcription	Small Intestine	intestine
8	chr6:74339200-74362800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:74341600-74362800	Weak transcription	Esophagus	oesophagus
10	chr6:74341600-74362800	Weak transcription	Gastric	stomach
11	chr6:74341800-74362600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:74342000-74362800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:74342400-74362800	Weak transcription	Lung	lung
14	chr6:74342400-74362800	Weak transcription	Spleen	Spleen
15	chr6:74343200-74362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:74346000-74362200	Weak transcription	Hela-S3	cervix
17	chr6:74347200-74362800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:74349000-74361600	Weak transcription	Dnd41	blood
19	chr6:74349600-74362800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:74350600-74362600	Weak transcription	Fetal Heart	heart
21	chr6:74351600-74362400	Weak transcription	Right Ventricle	heart
22	chr6:74352600-74361600	Weak transcription	Liver	Liver
23	chr6:74355600-74361800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:74355600-74362400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:74355600-74362400	Weak transcription	Thymus	Thymus
26	chr6:74355600-74362800	Weak transcription	Left Ventricle	heart
27	chr6:74355800-74361600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:74355800-74361600	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:74355800-74361800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:74355800-74361800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:74355800-74361800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:74355800-74362000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:74355800-74362000	Weak transcription	Brain Anterior Caudate	brain
34	chr6:74355800-74362000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:74355800-74362200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:74355800-74362400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:74355800-74362400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:74355800-74362400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:74355800-74362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:74355800-74362400	Weak transcription	Brain Angular Gyrus	brain
41	chr6:74355800-74362400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:74355800-74362400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:74355800-74362400	Weak transcription	Fetal Thymus	thymus
44	chr6:74355800-74362400	Weak transcription	Psoas Muscle	Psoas
45	chr6:74355800-74362600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:74355800-74362600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:74355800-74362600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:74355800-74362600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:74355800-74362600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:74355800-74362600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links