Variant report

Variant	rs853418
Chromosome Location	chr6:4113268-4113269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4111554..4114188-chr6:4116120..4118863,4	K562	blood:
2	chr6:4112616..4115686-chr6:4134905..4137103,3	MCF-7	breast:
3	chr6:4112263..4113921-chr6:4124338..4126285,2	K562	blood:
4	chr6:4112632..4117025-chr6:4117179..4121716,5	K562	blood:
5	chr6:4108578..4110178-chr6:4111693..4114473,2	K562	blood:

Variant related genes	Relation type
ENSG00000254821	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs101418	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11751668	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11755877	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1204951	0.84[ASN][1000 genomes]
rs2326408	0.91[ASN][1000 genomes]
rs2745455	0.82[ASN][1000 genomes]
rs2783063	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2783073	0.91[ASN][1000 genomes]
rs28878015	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4443542	0.83[EUR][1000 genomes]
rs4959271	0.98[ASN][1000 genomes]
rs582008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs583782	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]
rs583881	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]
rs584585	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs608195	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs611500	0.91[ASN][1000 genomes]
rs612022	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs612477	0.86[ASN][1000 genomes]
rs613028	0.88[ASN][1000 genomes]
rs613260	0.91[ASN][1000 genomes]
rs613709	0.91[ASN][1000 genomes]
rs617604	0.82[ASN][1000 genomes]
rs617790	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs619439	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs619483	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs619873	0.91[ASN][1000 genomes]
rs620484	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs621205	0.99[ASN][1000 genomes]
rs626080	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs627259	0.86[ASN][1000 genomes]
rs629362	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs633290	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs634114	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs634698	0.83[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs634970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638329	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs643232	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs646385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648900	0.91[ASN][1000 genomes]
rs649725	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs654982	0.82[JPT][hapmap]
rs659025	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs659051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659305	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs660560	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs660957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661404	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs661657	0.84[ASN][1000 genomes]
rs662834	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs664299	0.89[ASN][1000 genomes]
rs664635	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]
rs664898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665894	0.82[ASN][1000 genomes]
rs666254	0.82[JPT][hapmap]
rs668070	0.81[ASN][1000 genomes]
rs674543	0.81[ASN][1000 genomes]
rs676683	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs678285	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]
rs679303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689308	0.91[ASN][1000 genomes]
rs694058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694903	0.86[ASN][1000 genomes]
rs707991	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7166	0.91[ASN][1000 genomes]
rs7744628	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7757606	0.91[ASN][1000 genomes]
rs853416	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs853417	0.91[ASN][1000 genomes]
rs9328220	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9392560	1.00[YRI][hapmap]
rs9405219	0.84[ASN][1000 genomes]
rs9405701	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4102600-4113800	Weak transcription	Psoas Muscle	Psoas
2	chr6:4103400-4115400	Weak transcription	Fetal Brain Male	brain
3	chr6:4103400-4115600	Weak transcription	Fetal Stomach	stomach
4	chr6:4103400-4115600	Weak transcription	Gastric	stomach
5	chr6:4104600-4115600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:4104600-4115600	Weak transcription	Pancreas	Pancrea
7	chr6:4104800-4115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:4104800-4115200	Weak transcription	HMEC	breast
9	chr6:4105000-4113600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:4107200-4114800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:4109000-4115600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:4109200-4115600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:4110200-4113800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:4110200-4114600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:4110400-4115400	Weak transcription	Fetal Kidney	kidney
16	chr6:4110400-4115600	Weak transcription	Ovary	ovary
17	chr6:4110400-4118400	Weak transcription	A549	lung
18	chr6:4110400-4124400	Weak transcription	Fetal Heart	heart
19	chr6:4110600-4115400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:4110600-4115400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:4110600-4115600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:4110600-4115600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:4110600-4115600	Weak transcription	Fetal Intestine Large	intestine
24	chr6:4110600-4115600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:4110600-4115800	Weak transcription	Small Intestine	intestine
26	chr6:4110800-4113400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:4110800-4115200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:4110800-4115600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:4110800-4115600	Weak transcription	HUVEC	blood vessel
30	chr6:4111000-4113600	Weak transcription	HepG2	liver
31	chr6:4111000-4115600	Weak transcription	NHEK	skin
32	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
33	chr6:4111200-4115600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:4111400-4113600	Weak transcription	Osteobl	bone
35	chr6:4111800-4114200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:4112400-4115200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:4112600-4114400	Weak transcription	Fetal Thymus	thymus
38	chr6:4112800-4113400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:4112800-4113600	ZNF genes & repeats	Brain Anterior Caudate	brain
40	chr6:4113000-4113800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:4113000-4115200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:4113200-4113600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr6:4113200-4114200	Weak transcription	Primary T cells from cord blood	blood
44	chr6:4113200-4114600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:4113200-4115400	Weak transcription	Fetal Brain Female	brain
46	chr6:4113200-4115400	Weak transcription	GM12878-XiMat	blood
47	chr6:4113200-4115600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:4113200-4115600	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links