Variant report

Variant	rs653536
Chromosome Location	chr6:33660411-33660412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33657954..33660672-chr6:33660957..33664215,4	MCF-7	breast:
2	chr6:33587314..33592159-chr6:33656861..33661736,6	K562	blood:
3	chr6:33659672..33661992-chr6:33673865..33675730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction
ENSG00000269490	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2229638	0.89[YRI][hapmap]
rs4711333	1.00[CHD][hapmap]
rs4713647	1.00[CHD][hapmap]
rs485623	1.00[CHD][hapmap]
rs523076	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs525623	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs557559	1.00[CHD][hapmap]
rs559290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560218	1.00[CHD][hapmap]
rs572708	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs62398913	0.93[EUR][1000 genomes]
rs637135	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653825	0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880503	0.85[EUR][1000 genomes]
rs7757722	1.00[CHD][hapmap]
rs791900	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs942637	1.00[ASW][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
2	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:33621400-33672600	Strong transcription	Dnd41	blood
5	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:33630400-33660800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr6:33631800-33661200	Weak transcription	Liver	Liver
10	chr6:33636600-33660600	Strong transcription	Colonic Mucosa	Colon
11	chr6:33636800-33661400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:33637400-33661600	Strong transcription	Esophagus	oesophagus
13	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:33641200-33661600	Strong transcription	NHEK	skin
16	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:33641800-33661800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:33642400-33660600	Weak transcription	Brain Germinal Matrix	brain
19	chr6:33644000-33660600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:33644000-33662000	Weak transcription	Fetal Kidney	kidney
21	chr6:33649600-33660600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:33649800-33661400	Strong transcription	Pancreas	Pancrea
23	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:33651600-33660600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:33652000-33661800	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:33653600-33661800	Strong transcription	Hela-S3	cervix
29	chr6:33653800-33660600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:33654000-33660800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:33654600-33661600	Weak transcription	Fetal Brain Female	brain
32	chr6:33654800-33661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:33654800-33662600	Weak transcription	Small Intestine	intestine
34	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
36	chr6:33656400-33661600	Strong transcription	A549	lung
37	chr6:33656400-33662600	Weak transcription	Brain Substantia Nigra	brain
38	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
39	chr6:33657000-33660800	Weak transcription	Fetal Brain Male	brain
40	chr6:33657000-33661400	Weak transcription	Ovary	ovary
41	chr6:33658000-33660600	Enhancers	Fetal Heart	heart
42	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
43	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr6:33658200-33660800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr6:33658400-33661000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:33658400-33661800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:33658800-33662600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin

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