Variant report

Variant	rs5752795
Chromosome Location	chr22:29178820-29178821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29136406..29138475-chr22:29177322..29179599,3	MCF-7	breast:
2	chr22:29167480..29169937-chr22:29178335..29181133,3	MCF-7	breast:
3	chr22:29175785..29179613-chr22:29195586..29198060,4	K562	blood:
4	chr22:29172058..29177577-chr22:29178390..29181662,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12628211	0.94[ASN][1000 genomes]
rs2097461	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239815	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269577	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347447	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881635	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35259224	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788409	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752801	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752804	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752807	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752809	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752812	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752813	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762795	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762803	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762815	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762824	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762825	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762853	0.83[ASN][1000 genomes]
rs5762854	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5762863	0.84[ASN][1000 genomes]
rs5762864	0.84[ASN][1000 genomes]
rs5997408	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005867	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005869	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005872	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005881	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005892	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005916	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005927	0.81[ASN][1000 genomes]
rs6005929	0.83[ASN][1000 genomes]
rs7287124	0.94[ASN][1000 genomes]
rs7287806	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763073	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8137969	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625566	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625588	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5752795	CCDC117	Cis_1M	lymphoblastoid	RTeQTL
rs5752795	XBP1	Cis_1M	lymphoblastoid	RTeQTL

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	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
11	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
13	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
20	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr22:29171000-29179600	Weak transcription	Small Intestine	intestine
22	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr22:29171200-29179000	Weak transcription	Brain Substantia Nigra	brain
24	chr22:29171200-29179200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:29171200-29188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:29171400-29179600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:29171400-29186000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:29171800-29186200	Strong transcription	Fetal Thymus	thymus
30	chr22:29172000-29179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr22:29172200-29179600	Weak transcription	NHLF	lung
32	chr22:29172400-29179200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr22:29172400-29179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr22:29172400-29186200	Strong transcription	Placenta	Placenta
35	chr22:29172600-29184200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr22:29173200-29185600	Strong transcription	Left Ventricle	heart
37	chr22:29173600-29179200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr22:29173800-29185600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
40	chr22:29175000-29183600	Strong transcription	Dnd41	blood
41	chr22:29175000-29186000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr22:29175200-29179800	Strong transcription	Fetal Lung	lung
43	chr22:29175400-29184200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:29175400-29185600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr22:29175600-29179200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr22:29175600-29182200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr22:29175600-29183600	Strong transcription	Primary B cells from cord blood	blood
48	chr22:29175600-29184800	Strong transcription	Thymus	Thymus
49	chr22:29175600-29185800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr22:29175800-29185200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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