Variant report

Variant	rs639768
Chromosome Location	chr11:74723556-74723557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74721191..74723681-chr11:74738693..74740282,2	K562	blood:
2	chr11:74720689..74723993-chr11:74726887..74730730,4	K562	blood:
3	chr11:74697161..74701589-chr11:74722600..74726344,4	K562	blood:
4	chr11:74718195..74720247-chr11:74720638..74725199,4	K562	blood:
5	chr11:74663493..74665057-chr11:74721622..74724251,2	K562	blood:
6	chr11:74723507..74725888-chr11:74813976..74816359,2	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11236291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12287793	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3018833	0.89[ASN][1000 genomes]
rs487226	0.81[JPT][hapmap]
rs493001	0.81[JPT][hapmap]
rs494474	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4944962	0.81[JPT][hapmap]
rs514534	0.81[JPT][hapmap]
rs517666	0.81[JPT][hapmap]
rs522808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565377	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs566480	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568310	0.91[ASN][1000 genomes]
rs58778107	0.96[ASN][1000 genomes]
rs58972415	0.85[ASN][1000 genomes]
rs59860682	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605954	0.81[JPT][hapmap]
rs629191	0.81[JPT][hapmap]
rs650130	0.81[JPT][hapmap]
rs662062	0.81[JPT][hapmap]
rs670246	0.81[JPT][hapmap]
rs671544	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs674122	0.93[ASN][1000 genomes]
rs681566	0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs685116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693212	0.80[JPT][hapmap]
rs7128833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939123	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952096	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952209	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs639768	XRRA1	cis	lymphoblastoid	seeQTL
rs639768	XRRA1	cis	parietal	SCAN
rs639768	IL18BP	cis	cerebellum	SCAN
rs639768	FCHSD2	cis	cerebellum	SCAN
rs639768	PAAF1	cis	cerebellum	SCAN
rs639768	KCTD21	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74700600-74725000	Weak transcription	HSMMtube	muscle
2	chr11:74701000-74723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:74712000-74728200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:74714200-74725400	Strong transcription	Dnd41	blood
5	chr11:74714800-74725000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:74715000-74723600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:74715000-74724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:74715400-74723600	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr11:74715400-74723800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:74715600-74723600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:74715600-74725400	Strong transcription	Liver	Liver
12	chr11:74716200-74724000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:74716200-74724000	Strong transcription	GM12878-XiMat	blood
14	chr11:74716200-74725600	Strong transcription	Primary T cells from cord blood	blood
15	chr11:74716400-74723600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:74716400-74723800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:74716400-74724000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:74716400-74724200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:74716400-74725600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:74716400-74725600	Strong transcription	Thymus	Thymus
21	chr11:74717400-74724400	Strong transcription	Fetal Thymus	thymus
22	chr11:74717600-74725400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:74717600-74726000	Weak transcription	Esophagus	oesophagus
24	chr11:74718000-74723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:74718000-74724000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:74718000-74724400	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:74718000-74733800	Weak transcription	Brain Substantia Nigra	brain
28	chr11:74718000-74734200	Weak transcription	Right Ventricle	heart
29	chr11:74718200-74726200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:74718200-74726200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:74718200-74729200	Weak transcription	Gastric	stomach
32	chr11:74718400-74726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:74718400-74729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:74718600-74724000	Weak transcription	NHDF-Ad	bronchial
35	chr11:74718600-74725800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:74718800-74724400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:74718800-74726600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:74719000-74725000	Weak transcription	HMEC	breast
39	chr11:74719200-74725000	Weak transcription	Hela-S3	cervix
40	chr11:74719400-74724000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:74719400-74728600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:74719800-74724000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:74720000-74724000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr11:74720400-74725400	Weak transcription	NH-A	brain
45	chr11:74721000-74724000	Weak transcription	Osteobl	bone
46	chr11:74721000-74724400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:74721000-74724400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:74721000-74724400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr11:74721000-74726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:74721200-74723800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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