Variant report

Variant	rs485804
Chromosome Location	chr6:13416010-13416011
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	chr6:13396704..13399515-chr6:13413657..13416189,2	K562	blood:
2	chr6:13415611..13418241-chr6:13485753..13488399,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10807437	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11758233	0.82[ASN][1000 genomes]
rs1345031	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1345032	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550520	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1550521	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2119481	0.95[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2119482	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2119483	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2119484	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165419	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4454121	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715251	0.83[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4715261	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs476138	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487607	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs488885	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490443	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494026	0.81[ASN][1000 genomes]
rs500197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs503117	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs508153	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs513613	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs519657	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs519890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520828	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs536916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs536998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs546507	0.86[ASN][1000 genomes]
rs550403	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558126	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs558242	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559565	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs559612	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs563424	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs563662	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565013	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs566320	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62386724	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6458814	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6458815	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6910652	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7742086	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs821298	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs821299	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821300	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357720	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9370104	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9395768	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9474117	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:13408600-13422600	Weak transcription	HSMM	muscle
5	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:13410400-13416400	Enhancers	Right Atrium	heart
9	chr6:13411400-13416200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
11	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
13	chr6:13412200-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:13412800-13416800	Enhancers	Brain Substantia Nigra	brain
15	chr6:13413200-13417800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:13413600-13419400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:13413600-13419800	Weak transcription	Esophagus	oesophagus
18	chr6:13413800-13417800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:13413800-13419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:13414000-13420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:13414000-13421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:13414000-13421800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:13414000-13421800	Weak transcription	Brain Germinal Matrix	brain
24	chr6:13414000-13422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:13414200-13417800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:13414600-13422000	Weak transcription	NHLF	lung
27	chr6:13414800-13419200	Weak transcription	Fetal Brain Female	brain
28	chr6:13414800-13420200	Weak transcription	HSMMtube	muscle
29	chr6:13415000-13416600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:13415000-13417000	Weak transcription	Brain Anterior Caudate	brain
31	chr6:13415000-13417800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:13415000-13418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:13415000-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:13415000-13419200	Weak transcription	NHEK	skin
35	chr6:13415000-13420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:13415000-13420400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:13415200-13417800	Weak transcription	Adipose Nuclei	Adipose
38	chr6:13415200-13418800	Weak transcription	Fetal Brain Male	brain
39	chr6:13415200-13419400	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:13415200-13419600	Weak transcription	Primary T cells from cord blood	blood
41	chr6:13415200-13420200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:13415400-13417000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:13415400-13417200	Weak transcription	Brain Angular Gyrus	brain
44	chr6:13415400-13417600	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:13415400-13419000	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:13415400-13419200	Weak transcription	Fetal Stomach	stomach
47	chr6:13415400-13419400	Weak transcription	Fetal Lung	lung
48	chr6:13415400-13422600	Weak transcription	Gastric	stomach
49	chr6:13415600-13417200	Weak transcription	HepG2	liver
50	chr6:13415600-13417800	Weak transcription	Pancreas	Pancrea

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