Variant report

Variant	rs602399
Chromosome Location	chr6:33713779-33713780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33710698..33713860-chr6:33753568..33757560,4	MCF-7	breast:
2	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:
3	chr6:33700581..33702116-chr6:33711630..33713944,2	K562	blood:
4	chr6:33712841..33714419-chr6:33746721..33749211,2	K562	blood:
5	chr6:33711726..33713871-chr6:33755985..33757617,2	K562	blood:
6	chr6:33711077..33714000-chr6:33723904..33727038,3	MCF-7	breast:
7	chr6:33712629..33714583-chr6:33734231..33736589,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.94[CEU][hapmap]
rs10947436	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947446	0.83[CEU][hapmap]
rs11751943	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1536500	0.84[EUR][1000 genomes]
rs1536501	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547668	0.84[ASW][hapmap];0.89[CEU][hapmap];0.83[LWK][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1998949	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2182658	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2182659	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395401	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395447	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2967	1.00[JPT][hapmap]
rs4711350	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996879	0.81[EUR][1000 genomes]
rs530614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][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]
rs549652	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs570749	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs597723	0.90[EUR][1000 genomes]
rs608971	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs623813	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs652049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs680608	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684119	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs688209	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs751727	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756138	0.92[YRI][hapmap]
rs756139	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs764753	1.00[JPT][hapmap]
rs7739273	0.91[YRI][hapmap]
rs7752348	0.91[EUR][1000 genomes]
rs791904	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs942496	0.84[ASW][hapmap];0.83[CEU][hapmap];0.85[LWK][hapmap]
rs943463	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943472	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs943476	1.00[ASW][hapmap];0.96[YRI][hapmap]
rs9461905	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9461907	0.83[EUR][1000 genomes]
rs9469542	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs602399	C6orf125	cis	cerebellum	SCAN
rs602399	BAK1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33706600-33715800	Enhancers	Fetal Intestine Large	intestine
2	chr6:33707400-33714000	Weak transcription	Spleen	Spleen
3	chr6:33710600-33715200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:33710800-33714200	Enhancers	Pancreas	Pancrea
5	chr6:33710800-33716600	Active TSS	Psoas Muscle	Psoas
6	chr6:33711200-33715600	Enhancers	Fetal Intestine Small	intestine
7	chr6:33711600-33713800	Enhancers	Placenta	Placenta
8	chr6:33711600-33714000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr6:33711600-33714200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:33711800-33713800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:33711800-33713800	Enhancers	Colonic Mucosa	Colon
12	chr6:33711800-33713800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
13	chr6:33711800-33714400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:33711800-33714600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:33711800-33714600	Enhancers	NHEK	skin
16	chr6:33711800-33715000	Active TSS	Left Ventricle	heart
17	chr6:33711800-33715200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:33711800-33715600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:33711800-33715800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:33712000-33713800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:33712000-33714000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:33712000-33714400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:33712000-33714600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:33712000-33714600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:33712000-33715000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:33712000-33715400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr6:33712000-33717000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:33712000-33717800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:33712200-33713800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:33712200-33714400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:33712200-33714800	Enhancers	Fetal Stomach	stomach
32	chr6:33712200-33714800	Active TSS	Right Atrium	heart
33	chr6:33712200-33715200	Enhancers	NHLF	lung
34	chr6:33712400-33713800	Enhancers	Fetal Kidney	kidney
35	chr6:33712400-33713800	Enhancers	Fetal Lung	lung
36	chr6:33712400-33713800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr6:33712400-33714000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:33712400-33714200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:33712400-33714200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:33712400-33714400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:33712400-33714600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:33712400-33714800	Active TSS	Right Ventricle	heart
43	chr6:33712400-33714800	Enhancers	A549	lung
44	chr6:33712400-33715000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr6:33712400-33715000	Active TSS	Brain Hippocampus Middle	brain
46	chr6:33712400-33715000	Active TSS	Brain Substantia Nigra	brain
47	chr6:33712400-33715600	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:33712400-33719600	Weak transcription	Gastric	stomach
49	chr6:33712600-33713800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:33712600-33714400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links