Variant report

Variant	rs6457894
Chromosome Location	chr6:36188580-36188581
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36173638..36177539-chr6:36188000..36190986,3	MCF-7	breast:
2	chr6:36187119..36188817-chr6:36194570..36197402,2	MCF-7	breast:
3	chr6:36168123..36171396-chr6:36185639..36189753,3	K562	blood:
4	chr6:36163834..36166808-chr6:36185455..36188870,4	MCF-7	breast:
5	chr6:36187527..36189506-chr6:36193052..36195234,2	MCF-7	breast:
6	chr6:36187149..36188865-chr6:36189489..36192331,2	MCF-7	breast:
7	chr6:36163727..36165566-chr6:36187260..36189115,2	K562	blood:
8	chr6:36181281..36186004-chr6:36187073..36191196,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10807157	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs10947591	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196677	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12197499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13196184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17356524	1.00[JPT][hapmap]
rs2032506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234075	1.00[CHB][hapmap]
rs2301422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815808	1.00[YRI][hapmap]
rs34262487	1.00[ASN][1000 genomes]
rs4236048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711434	1.00[YRI][hapmap]
rs6457883	1.00[YRI][hapmap]
rs6457884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6457892	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906612	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs6927278	1.00[YRI][hapmap]
rs71569325	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7747793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773924	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366900	0.83[EUR][1000 genomes]
rs9470228	0.93[CEU][hapmap];0.83[EUR][1000 genomes]

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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6457894	RP1-179N16.6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36164400-36203000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36166200-36192200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr6:36166600-36200200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:36166800-36201800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:36167000-36201800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36167200-36201400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:36167400-36191600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:36167400-36201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:36167600-36199800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:36167600-36201200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:36167800-36192000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:36167800-36201400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr6:36168000-36190600	Strong transcription	HSMM	muscle
14	chr6:36168000-36191200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:36168000-36192400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:36168000-36196800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:36168000-36200400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr6:36168000-36201400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:36168200-36188800	Strong transcription	HUVEC	blood vessel
20	chr6:36168200-36195400	Strong transcription	Placenta	Placenta
21	chr6:36169400-36201800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:36169600-36188800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:36170000-36201800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:36171200-36188600	Strong transcription	Colon Smooth Muscle	Colon
25	chr6:36172200-36202000	Strong transcription	Thymus	Thymus
26	chr6:36172600-36201400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr6:36172600-36201600	Strong transcription	Liver	Liver
28	chr6:36172600-36202000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:36172800-36195200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:36172800-36195600	Strong transcription	Fetal Thymus	thymus
31	chr6:36173000-36201200	Strong transcription	Dnd41	blood
32	chr6:36173400-36188600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:36173400-36202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:36173800-36188800	Strong transcription	Brain Substantia Nigra	brain
35	chr6:36174000-36188600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:36174000-36204600	Strong transcription	Primary T cells from cord blood	blood
37	chr6:36174200-36201800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr6:36174400-36201600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:36178600-36192000	Strong transcription	HepG2	liver
40	chr6:36179400-36197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:36180000-36190600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:36180400-36189800	Weak transcription	Psoas Muscle	Psoas
43	chr6:36180400-36196200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr6:36183400-36190200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:36183400-36194800	Genic enhancers	Fetal Intestine Large	intestine
46	chr6:36183600-36199200	Genic enhancers	Fetal Intestine Small	intestine
47	chr6:36184000-36189800	Weak transcription	A549	lung
48	chr6:36184200-36188800	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr6:36184400-36190800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:36184800-36192600	Strong transcription	GM12878-XiMat	blood

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