Variant report

Variant	rs138638
Chromosome Location	chr22:28380588-28380589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28361846..28364536-chr22:28378435..28381037,2	K562	blood:
2	chr22:28378900..28382846-chr22:28384194..28387433,3	K562	blood:
3	chr22:28315267..28317072-chr22:28379506..28381389,2	MCF-7	breast:
4	chr22:28371840..28377290-chr22:28378156..28383171,5	K562	blood:

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction
ENSG00000100154	Chromatin interaction
ENSG00000264073	Chromatin interaction
ENSG00000180957	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1028364	0.81[JPT][hapmap]
rs118839	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12171034	0.87[ASN][1000 genomes]
rs138631	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs138650	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs138675	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs138683	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs138685	0.93[CHD][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs1548235	0.88[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2038158	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2092054	0.93[ASN][1000 genomes]
rs2267121	0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[TSI][hapmap]
rs3747141	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4140571	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs470100	0.83[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs470105	0.85[CHD][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752667	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762416	0.90[EUR][1000 genomes]
rs5762418	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997319	0.82[CHB][hapmap]
rs6005671	0.89[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs720621	0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[TSI][hapmap]
rs73425788	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs738451	0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap]
rs7625	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs957601	0.91[EUR][1000 genomes]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv522306	chr22:28378472-28402624	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs138638	CHEK2	cis	cerebellum	SCAN
rs138638	ZNF280A	cis	cerebellum	SCAN
rs138638	SEZ6L	cis	cerebellum	SCAN
rs138638	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28318800-28382000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr22:28319600-28383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr22:28355400-28387800	Weak transcription	Fetal Brain Male	brain
4	chr22:28360200-28382800	Weak transcription	HSMM	muscle
5	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr22:28368400-28383400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr22:28368800-28385800	Weak transcription	Brain Angular Gyrus	brain
8	chr22:28369000-28381200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
10	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr22:28370400-28382400	Weak transcription	Stomach Mucosa	stomach
12	chr22:28370400-28387200	Weak transcription	Fetal Kidney	kidney
13	chr22:28371800-28386800	Weak transcription	NHDF-Ad	bronchial
14	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
15	chr22:28372000-28382600	Weak transcription	NH-A	brain
16	chr22:28372000-28382800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr22:28372000-28386400	Weak transcription	HUVEC	blood vessel
18	chr22:28372800-28380600	Weak transcription	Brain Substantia Nigra	brain
19	chr22:28372800-28382000	Weak transcription	K562	blood
20	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:28373800-28383000	Strong transcription	Dnd41	blood
22	chr22:28373800-28386400	Strong transcription	Fetal Muscle Leg	muscle
23	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
24	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
25	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
26	chr22:28374600-28386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr22:28376200-28382600	Strong transcription	Brain Germinal Matrix	brain
28	chr22:28376400-28383800	Strong transcription	Ovary	ovary
29	chr22:28376600-28382600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr22:28376800-28383600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:28377000-28381800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr22:28377000-28383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr22:28377000-28383400	Strong transcription	Placenta	Placenta
34	chr22:28377200-28383400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr22:28377200-28385800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:28377200-28386400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:28377200-28386800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr22:28377200-28386800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr22:28377200-28387200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr22:28377200-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:28377600-28382800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr22:28377600-28382800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr22:28377600-28383200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr22:28377800-28381200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:28377800-28382200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr22:28377800-28382200	Strong transcription	Brain Anterior Caudate	brain
47	chr22:28377800-28382200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr22:28377800-28382600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr22:28377800-28382800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr22:28377800-28383200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links