Variant report

Variant	rs9405701
Chromosome Location	chr6:4123441-4123442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4122249..4124669-chr6:4133973..4135561,2	MCF-7	breast:
2	chr6:4050000..4052650-chr6:4123056..4125495,2	K562	blood:

Variant related genes	Relation type
ENSG00000145975	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs101418	0.83[ASN][1000 genomes]
rs11751668	0.83[EUR][1000 genomes]
rs11755877	0.83[ASN][1000 genomes]
rs1204951	0.84[ASN][1000 genomes]
rs2326408	0.91[ASN][1000 genomes]
rs2745455	0.82[ASN][1000 genomes]
rs2783063	0.84[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[ASN][1000 genomes]
rs583782	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583881	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584585	0.91[ASN][1000 genomes]
rs608195	0.86[ASN][1000 genomes]
rs611500	0.91[ASN][1000 genomes]
rs612022	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	0.91[ASN][1000 genomes]
rs619439	0.91[ASN][1000 genomes]
rs619483	0.83[ASN][1000 genomes]
rs619873	0.91[ASN][1000 genomes]
rs620484	0.91[ASN][1000 genomes]
rs621205	0.99[ASN][1000 genomes]
rs626080	0.88[ASN][1000 genomes]
rs627259	0.86[ASN][1000 genomes]
rs629362	0.91[ASN][1000 genomes]
rs633290	0.91[ASN][1000 genomes]
rs634114	0.83[ASN][1000 genomes]
rs634698	0.91[ASN][1000 genomes]
rs634970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638329	1.00[ASN][1000 genomes]
rs643232	0.91[ASN][1000 genomes]
rs646385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648900	0.91[ASN][1000 genomes]
rs649725	0.91[ASN][1000 genomes]
rs659025	0.91[ASN][1000 genomes]
rs659051	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659305	0.91[ASN][1000 genomes]
rs660560	0.91[ASN][1000 genomes]
rs660957	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661404	0.91[ASN][1000 genomes]
rs661657	0.84[ASN][1000 genomes]
rs662834	0.83[ASN][1000 genomes]
rs664299	0.89[ASN][1000 genomes]
rs664635	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664898	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665894	0.82[ASN][1000 genomes]
rs668070	0.81[ASN][1000 genomes]
rs674543	0.81[ASN][1000 genomes]
rs676683	0.91[ASN][1000 genomes]
rs678285	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689308	0.91[ASN][1000 genomes]
rs694058	0.83[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	0.86[ASN][1000 genomes]
rs7166	0.91[ASN][1000 genomes]
rs7744628	0.91[ASN][1000 genomes]
rs7757606	0.91[ASN][1000 genomes]
rs853416	0.91[ASN][1000 genomes]
rs853417	0.91[ASN][1000 genomes]
rs853418	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328220	0.91[ASN][1000 genomes]
rs9405219	0.84[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4110400-4124400	Weak transcription	Fetal Heart	heart
2	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
3	chr6:4113800-4134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:4114000-4131400	Strong transcription	Brain Anterior Caudate	brain
5	chr6:4114200-4126200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:4114200-4132200	Strong transcription	Primary T cells from cord blood	blood
7	chr6:4114200-4132800	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:4114200-4133400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:4114400-4130200	Strong transcription	Liver	Liver
10	chr6:4114400-4131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:4114400-4132400	Strong transcription	Fetal Thymus	thymus
12	chr6:4114600-4125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:4114600-4126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:4114600-4130000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:4114600-4130600	Strong transcription	Brain Germinal Matrix	brain
16	chr6:4114600-4133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:4114800-4125600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:4114800-4132800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:4114800-4133400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr6:4115000-4125400	Strong transcription	NH-A	brain
21	chr6:4115200-4125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:4115200-4125800	Strong transcription	Adipose Nuclei	Adipose
23	chr6:4115200-4128600	Strong transcription	Brain Hippocampus Middle	brain
24	chr6:4115200-4129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:4115200-4131200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:4115200-4131200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:4115200-4132000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr6:4115200-4132000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:4115200-4132600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:4115200-4132800	Strong transcription	Left Ventricle	heart
31	chr6:4115200-4133000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:4115200-4133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:4115400-4124600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:4115400-4125000	Strong transcription	Osteobl	bone
35	chr6:4115400-4125400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:4115400-4129000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:4115400-4131000	Strong transcription	Fetal Brain Female	brain
38	chr6:4115400-4131200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:4115400-4131400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:4115400-4133200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:4115400-4133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:4115400-4133800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr6:4115600-4124200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:4115600-4124200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:4115600-4125600	Strong transcription	HepG2	liver
46	chr6:4115600-4125800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:4115600-4126400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:4115600-4129000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:4115600-4129400	Strong transcription	Brain Angular Gyrus	brain
50	chr6:4115600-4131000	Strong transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links