Variant report

Variant	rs2802699
Chromosome Location	chr6:69350299-69350300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69349314..69351973-chr6:69416825..69419613,2	K562	blood:
2	chr6:69349831..69353456-chr6:69358636..69362534,5	K562	blood:
3	chr6:69348595..69350906-chr6:69368329..69371179,2	K562	blood:
4	chr6:69343483..69346125-chr6:69348729..69350654,3	K562	blood:
5	chr6:69348216..69350779-chr6:69363202..69365467,2	K562	blood:
6	chr6:69342697..69344588-chr6:69349205..69351203,2	K562	blood:
7	chr6:69346849..69353858-chr6:69356877..69365508,11	K562	blood:

Variant related genes	Relation type
ENSG00000230910	Chromatin interaction
ENSG00000135298	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10806605	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs10945134	1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10945135	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12194992	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12196021	1.00[JPT][hapmap]
rs1523931	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs1523932	0.81[CHB][hapmap]
rs2024561	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2248272	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254150	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2256337	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2341765	0.83[ASN][1000 genomes]
rs2585593	0.80[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.82[TSI][hapmap]
rs2585594	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2585605	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2585616	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2585618	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585619	0.84[CHB][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2585620	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2746126	0.80[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2802690	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2802702	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2802703	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2802704	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2802705	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2802706	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2802710	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4554295	1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4607402	1.00[JPT][hapmap]
rs478070	0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs530888	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs639338	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6908159	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs9342729	1.00[JPT][hapmap]
rs9342730	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs9342731	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs9346233	0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs9346234	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9346237	1.00[JPT][hapmap]
rs9346238	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs9351734	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs9351735	0.87[CHB][hapmap]
rs9363962	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830680	chr6:69192214-69351103	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69342600-69351000	Active TSS	Brain Angular Gyrus	brain
2	chr6:69343200-69351200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:69343200-69352000	Active TSS	Brain Anterior Caudate	brain
4	chr6:69348600-69350400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:69348600-69352800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:69348800-69350600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:69349000-69350400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:69349000-69350800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:69349200-69350400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:69349200-69350400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:69349200-69350800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr6:69349200-69351000	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr6:69349400-69350400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:69349400-69350800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:69349400-69351000	Flanking Active TSS	K562	blood
16	chr6:69349600-69350400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:69349600-69350400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:69349600-69350600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:69349600-69350600	Active TSS	Fetal Kidney	kidney
20	chr6:69349600-69350800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:69349600-69350800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr6:69349600-69350800	Active TSS	Right Atrium	heart
23	chr6:69349600-69351600	Flanking Active TSS	Fetal Brain Female	brain
24	chr6:69349800-69350400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr6:69349800-69350400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr6:69349800-69350400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:69349800-69350400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:69349800-69350400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:69349800-69350400	Active TSS	Colonic Mucosa	Colon
30	chr6:69349800-69350400	Active TSS	Fetal Heart	heart
31	chr6:69349800-69350400	Active TSS	Psoas Muscle	Psoas
32	chr6:69349800-69350400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr6:69349800-69350600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:69349800-69350600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:69349800-69350600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:69349800-69350600	Flanking Bivalent TSS/Enh	Liver	Liver
37	chr6:69349800-69350600	Active TSS	Brain Cingulate Gyrus	brain
38	chr6:69349800-69350600	Active TSS	Colon Smooth Muscle	Colon
39	chr6:69349800-69350600	Active TSS	Fetal Muscle Trunk	muscle
40	chr6:69349800-69350600	Active TSS	Right Ventricle	heart
41	chr6:69349800-69350800	Active TSS	Brain Hippocampus Middle	brain
42	chr6:69349800-69350800	Flanking Active TSS	Fetal Stomach	stomach
43	chr6:69349800-69350800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr6:69349800-69350800	Active TSS	Rectal Smooth Muscle	rectum
45	chr6:69349800-69351000	Active TSS	Brain Substantia Nigra	brain
46	chr6:69350000-69350400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:69350000-69350400	Active TSS	Aorta	Aorta
48	chr6:69350000-69350400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
49	chr6:69350000-69350400	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:69350000-69350600	Bivalent Enhancer	Primary hematopoietic stem cells	blood

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