Variant report

Variant	rs6005879
Chromosome Location	chr22:29178314-29178315
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	chr22:29136406..29138475-chr22:29177322..29179599,3	MCF-7	breast:
2	chr22:29175785..29179613-chr22:29195586..29198060,4	K562	blood:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12159764	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs132530	0.96[YRI][hapmap]
rs1547424	0.80[ASN][1000 genomes]
rs16986714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269575	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41281601	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484131	0.83[ASN][1000 genomes]
rs4645087	0.80[ASN][1000 genomes]
rs57652775	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59954406	0.87[ASN][1000 genomes]
rs5997399	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005875	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005876	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005878	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005893	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005900	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005906	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005915	0.85[YRI][hapmap]
rs6005918	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005920	0.87[ASN][1000 genomes]
rs60513698	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6519764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7284322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290019	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290679	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290958	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291783	0.83[ASN][1000 genomes]
rs73388819	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388827	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388828	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388838	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73388841	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73399615	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73399621	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9941965	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	esv3517058	chr22:29176967-29179307	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv3517059	chr22:29176967-29179307	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv2430624	chr22:29177114-29178745	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
3	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
4	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
9	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
12	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
14	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
21	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr22:29171000-29179600	Weak transcription	Small Intestine	intestine
23	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:29171200-29178600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr22:29171200-29179000	Weak transcription	Brain Substantia Nigra	brain
26	chr22:29171200-29179200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:29171200-29188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:29171400-29179600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:29171400-29186000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:29171800-29186200	Strong transcription	Fetal Thymus	thymus
32	chr22:29172000-29179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr22:29172200-29179600	Weak transcription	NHLF	lung
34	chr22:29172400-29179200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:29172400-29179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:29172400-29186200	Strong transcription	Placenta	Placenta
37	chr22:29172600-29184200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr22:29173000-29178600	Weak transcription	A549	lung
39	chr22:29173200-29185600	Strong transcription	Left Ventricle	heart
40	chr22:29173600-29179200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr22:29173800-29185600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
43	chr22:29174000-29178600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:29174200-29178600	Weak transcription	Gastric	stomach
45	chr22:29175000-29183600	Strong transcription	Dnd41	blood
46	chr22:29175000-29186000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr22:29175200-29178600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr22:29175200-29179800	Strong transcription	Fetal Lung	lung
49	chr22:29175400-29184200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr22:29175400-29185600	Strong transcription	Primary T cells fromperipheralblood	blood

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