Variant report

Variant	rs6894123
Chromosome Location	chr5:114865876-114865877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114862754..114866326-chr5:114878456..114881611,5	MCF-7	breast:
2	chr5:114865115..114868183-chr5:114868722..114871711,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10038493	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10041776	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10043094	0.88[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs10053572	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10073505	0.81[ASN][1000 genomes]
rs10079000	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs1015812	0.88[ASN][1000 genomes]
rs12187973	0.82[CEU][hapmap]
rs13184723	0.87[ASN][1000 genomes]
rs13356084	0.94[ASN][1000 genomes]
rs13357862	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2032842	0.82[CHB][hapmap]
rs2546484	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546487	0.85[CEU][hapmap]
rs256938	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256956	0.80[CEU][hapmap]
rs256976	0.82[CEU][hapmap]
rs256977	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256989	0.86[ASN][1000 genomes]
rs256995	0.84[ASN][1000 genomes]
rs372702	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860557	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878790	0.80[ASN][1000 genomes]
rs6892071	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6893854	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];0.99[ASN][1000 genomes]
rs746566	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs766454	0.87[ASN][1000 genomes]
rs813761	0.80[CEU][hapmap]
rs9326964	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114854600-114870200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:114856800-114871000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:114857600-114866400	Strong transcription	Dnd41	blood
4	chr5:114857800-114877200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:114858600-114878800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:114858800-114876200	Weak transcription	Fetal Stomach	stomach
7	chr5:114859200-114866200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:114859200-114867200	Weak transcription	Fetal Intestine Small	intestine
9	chr5:114860800-114874000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:114860800-114877200	Weak transcription	Colonic Mucosa	Colon
11	chr5:114861000-114878600	Weak transcription	Pancreas	Pancrea
12	chr5:114861000-114878800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:114861000-114878800	Weak transcription	Spleen	Spleen
14	chr5:114861200-114871200	Weak transcription	Fetal Lung	lung
15	chr5:114861200-114871600	Weak transcription	HSMMtube	muscle
16	chr5:114861200-114872400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:114861200-114874200	Weak transcription	Aorta	Aorta
18	chr5:114861200-114875800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:114861200-114878600	Weak transcription	Esophagus	oesophagus
20	chr5:114861400-114866200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:114861400-114866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:114861400-114866200	Weak transcription	Osteobl	bone
23	chr5:114861400-114867200	Weak transcription	K562	blood
24	chr5:114861400-114868400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:114861400-114869400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:114861400-114871200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:114861400-114871200	Weak transcription	Fetal Kidney	kidney
28	chr5:114861400-114871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:114861400-114874200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:114861400-114874600	Weak transcription	Thymus	Thymus
31	chr5:114861400-114875400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:114861400-114877200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:114861600-114867800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:114861600-114868600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:114861600-114871600	Weak transcription	Placenta	Placenta
36	chr5:114861600-114874200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:114861800-114867200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:114861800-114871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:114862000-114866200	Weak transcription	NHEK	skin
40	chr5:114862000-114867000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:114862600-114867000	Weak transcription	HUVEC	blood vessel
42	chr5:114862800-114866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:114862800-114866000	Weak transcription	HMEC	breast
44	chr5:114862800-114866200	Weak transcription	Fetal Heart	heart
45	chr5:114862800-114866200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:114862800-114867000	Weak transcription	A549	lung
47	chr5:114862800-114867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:114862800-114867400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:114862800-114870200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:114862800-114871000	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links