Variant report

Variant	rs11153674
Chromosome Location	chr6:117869286-117869287
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:117802435..117804149-chr6:117867844..117870833,3	MCF-7	breast:
2	chr6:117868602..117871781-chr6:117879048..117881527,3	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456911	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456912	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457319	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457320	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484301	1.00[CHB][hapmap]
rs10872154	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153691	0.85[EUR][1000 genomes]
rs11758156	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759685	0.81[EUR][1000 genomes]
rs12191882	0.81[EUR][1000 genomes]
rs12192117	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192219	0.81[EUR][1000 genomes]
rs12193035	1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194014	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196716	1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196946	0.82[EUR][1000 genomes]
rs12197399	1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200953	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202612	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12205852	1.00[CHB][hapmap]
rs12208894	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209222	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209476	0.85[EUR][1000 genomes]
rs12209927	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210860	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12215701	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374604	0.85[EUR][1000 genomes]
rs17637404	1.00[CHB][hapmap]
rs17818735	1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134088	1.00[CHB][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41291926	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965600	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967203	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967214	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967253	0.85[EUR][1000 genomes]
rs916305	1.00[CHB][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929059	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320605	1.00[CHB][hapmap]
rs9481727	1.00[CHB][hapmap]
rs9489143	1.00[CHB][hapmap]
rs9489220	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688605	1.00[CHB][hapmap]
rs9766117	1.00[CHB][hapmap]
rs9766656	1.00[CHB][hapmap]
rs9766945	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9766959	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9767675	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117823200-117869600	Weak transcription	Small Intestine	intestine
2	chr6:117836600-117869600	Weak transcription	Stomach Mucosa	stomach
3	chr6:117846800-117869600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:117858200-117870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:117859800-117869400	Strong transcription	Fetal Intestine Large	intestine
6	chr6:117861000-117869600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:117862800-117869800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:117863400-117872200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:117863600-117869600	Genic enhancers	A549	lung
10	chr6:117864000-117870200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:117865200-117869400	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr6:117865600-117870600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:117866200-117869600	Strong transcription	Gastric	stomach
14	chr6:117866400-117869800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:117866600-117870400	Weak transcription	K562	blood
16	chr6:117867000-117869400	Strong transcription	HepG2	liver
17	chr6:117867000-117869600	Strong transcription	Liver	Liver
18	chr6:117867400-117869800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:117867400-117869800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:117868200-117872000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:117868400-117869600	Genic enhancers	HUVEC	blood vessel
22	chr6:117868600-117869400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:117868600-117869400	Enhancers	NH-A	brain
24	chr6:117868600-117869600	Enhancers	Fetal Heart	heart
25	chr6:117868600-117869800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr6:117868600-117869800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:117868600-117870200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr6:117868600-117870400	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:117868600-117870400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:117868600-117870600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr6:117868600-117871000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr6:117868600-117872400	Genic enhancers	NHEK	skin
33	chr6:117868800-117869400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:117868800-117869400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
35	chr6:117868800-117869400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:117868800-117869400	Active TSS	Brain Angular Gyrus	brain
37	chr6:117868800-117869400	Active TSS	Brain Cingulate Gyrus	brain
38	chr6:117868800-117869400	Active TSS	Brain Germinal Matrix	brain
39	chr6:117868800-117869400	Active TSS	Rectal Smooth Muscle	rectum
40	chr6:117868800-117869600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr6:117868800-117869600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:117868800-117869600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:117868800-117869600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:117868800-117869600	Active TSS	Brain Hippocampus Middle	brain
45	chr6:117868800-117869600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:117868800-117869600	Active TSS	Brain Substantia Nigra	brain
47	chr6:117868800-117869600	Flanking Active TSS	Fetal Thymus	thymus
48	chr6:117868800-117869600	Active TSS	Right Atrium	heart
49	chr6:117868800-117869600	Weak transcription	Hela-S3	cervix
50	chr6:117868800-117869800	Active TSS	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links