Variant report

Variant	rs6570620
Chromosome Location	chr6:144648125-144648126
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	chr6:144647226..144649891-chr6:144650190..144651852,2	MCF-7	breast:
2	chr6:144646379..144648634-chr6:144659334..144661793,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STX11-2	chr6:144648088-144648465	expReg_chr6_10714_+

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11970041	0.91[AMR][1000 genomes]
rs12178630	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073670	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2223428	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2328570	1.00[AMR][1000 genomes]
rs28737224	0.91[AMR][1000 genomes]
rs6570621	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6570631	1.00[MEX][hapmap]
rs6902637	0.91[AMR][1000 genomes]
rs6905106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932679	0.82[ASW][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9321971	1.00[AMR][1000 genomes]
rs9484865	1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484866	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484868	1.00[AMR][1000 genomes]
rs9484869	1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs9484870	0.91[AMR][1000 genomes]
rs9496924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496929	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496933	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9496934	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9496939	1.00[AMR][1000 genomes]
rs9496940	1.00[AMR][1000 genomes]
rs9496941	1.00[AMR][1000 genomes]
rs9496942	1.00[AMR][1000 genomes]
rs9496946	1.00[AMR][1000 genomes]
rs9496947	0.91[AMR][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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144630200-144648400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:144630600-144648200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:144635000-144651000	Weak transcription	Small Intestine	intestine
4	chr6:144635600-144650800	Weak transcription	Aorta	Aorta
5	chr6:144636000-144656200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:144636600-144654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:144636800-144650800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:144636800-144654800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:144636800-144656400	Weak transcription	Brain Substantia Nigra	brain
10	chr6:144637000-144651800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:144637400-144648400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:144639600-144660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:144642200-144654800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:144642200-144655200	Weak transcription	Thymus	Thymus
15	chr6:144642200-144659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:144642600-144649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:144643200-144651600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:144643600-144648200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:144643600-144651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:144643600-144652600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:144643600-144656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:144643800-144652000	Weak transcription	HSMM	muscle
23	chr6:144643800-144663000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:144644000-144648400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:144644400-144648200	Weak transcription	Osteobl	bone
26	chr6:144644400-144652600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:144644400-144652600	Weak transcription	NHDF-Ad	bronchial
28	chr6:144645400-144649200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:144645600-144649400	Genic enhancers	HepG2	liver
30	chr6:144646200-144651400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr6:144646400-144655200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:144646600-144649400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:144646600-144649600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr6:144646800-144652000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:144646800-144654600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:144647000-144648400	Enhancers	HUVEC	blood vessel
37	chr6:144647000-144650600	Weak transcription	Fetal Intestine Small	intestine
38	chr6:144647200-144649400	Enhancers	Fetal Heart	heart
39	chr6:144647400-144648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:144647400-144648800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:144647400-144649200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:144647400-144649400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:144647400-144649600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:144647600-144648200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:144647600-144648200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:144647600-144648200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:144647600-144649000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:144647600-144649200	Enhancers	Fetal Muscle Leg	muscle
49	chr6:144647800-144648200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:144647800-144648400	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links