Variant report

Variant	rs2232427
Chromosome Location	chr6:28359709-28359710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28317708..28320040-chr6:28358361..28360220,2	K562	blood:
2	chr6:28046681..28048670-chr6:28358880..28361224,2	K562	blood:
3	chr6:28303466..28305009-chr6:28358955..28361935,2	K562	blood:
4	chr6:28352795..28355228-chr6:28357917..28359743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005126	0.92[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11751928	0.92[CHB][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11755387	1.00[CHB][hapmap]
rs13190937	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs13193272	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13196606	0.91[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13199081	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203055	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13209596	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13215804	0.91[CHB][hapmap]
rs13217326	0.88[EUR][1000 genomes]
rs16894011	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16894091	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16894106	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17856167	1.00[CHB][hapmap]
rs1936365	0.80[CEU][hapmap]
rs213239	0.82[CHB][hapmap]
rs213241	0.81[CHB][hapmap]
rs213243	0.82[CHB][hapmap]
rs213244	0.81[CHB][hapmap]
rs28505234	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3799499	0.90[CHB][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799500	0.92[CHB][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57071502	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58020991	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902687	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs6905380	0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931359	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940744	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71559081	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740429	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750526	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7754960	0.92[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774981	0.91[CHB][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853676	0.80[CEU][hapmap]
rs853678	0.81[CEU][hapmap]
rs853679	0.80[CEU][hapmap]
rs853681	0.80[CEU][hapmap]
rs853685	0.80[CEU][hapmap]
rs9393908	0.81[CEU][hapmap]
rs9468345	0.82[CHB][hapmap]
rs9468356	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468358	0.92[CHB][hapmap];0.84[JPT][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468364	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs9969098	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2232427	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2232427	AL022393.7	cis	Muscle Skeletal	GTEx
rs2232427	ZSCAN23	cis	Artery Tibial	GTEx
rs2232427	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2232427	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2232427	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2232427	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28345000-28361600	Strong transcription	Dnd41	blood
2	chr6:28351600-28364600	Weak transcription	Right Atrium	heart
3	chr6:28352000-28362000	Strong transcription	Primary T cells from cord blood	blood
4	chr6:28352200-28365800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:28352400-28361400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:28352600-28361800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:28352600-28362000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28352600-28362600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:28352600-28364200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:28352600-28364400	Strong transcription	Fetal Thymus	thymus
11	chr6:28352600-28364600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:28352600-28365400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:28352600-28365800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:28352800-28361000	Strong transcription	Brain Anterior Caudate	brain
15	chr6:28353000-28361000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:28353000-28361000	Strong transcription	Fetal Intestine Large	intestine
17	chr6:28353000-28361400	Strong transcription	Brain Germinal Matrix	brain
18	chr6:28353000-28361600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:28353000-28361800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:28353000-28362200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:28353000-28364800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:28353200-28361200	Strong transcription	HepG2	liver
23	chr6:28353200-28361400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:28353200-28362000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:28353400-28361000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:28353400-28361200	Strong transcription	Liver	Liver
27	chr6:28353600-28360800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:28353800-28361200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28354000-28364600	Strong transcription	Fetal Muscle Leg	muscle
30	chr6:28354200-28361800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:28354200-28365600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr6:28354400-28361000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:28354400-28364800	Strong transcription	Fetal Stomach	stomach
34	chr6:28354800-28360800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28354800-28361400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:28354800-28363800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr6:28355000-28361000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:28355000-28361000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr6:28355000-28361200	Strong transcription	HMEC	breast
40	chr6:28355000-28361400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:28355000-28361600	Strong transcription	Brain Hippocampus Middle	brain
42	chr6:28355200-28361400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:28355400-28360800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:28355400-28361800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:28355600-28361000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:28355600-28361000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:28355600-28361000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:28355600-28361000	Strong transcription	Placenta	Placenta
49	chr6:28355600-28361600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr6:28355600-28362000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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