Variant report

Variant	rs13214023
Chromosome Location	chr6:28332141-28332142
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	chr6:28323337..28330678-chr6:28330738..28334657,8	K562	blood:
2	chr6:28331703..28333940-chr6:28336261..28337790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs13190888	0.88[EUR][1000 genomes]
rs13191038	0.93[EUR][1000 genomes]
rs13191786	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13195291	0.93[EUR][1000 genomes]
rs13197633	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13198809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13201308	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13201681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204012	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205211	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205911	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13207345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13208096	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13211507	1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13213152	1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217984	0.85[EUR][1000 genomes]
rs2232423	1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2232426	0.96[EUR][1000 genomes]
rs2232429	0.96[EUR][1000 genomes]
rs33932084	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34218844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34396849	0.93[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34546986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34661125	0.93[EUR][1000 genomes]
rs34676049	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34691223	0.93[EUR][1000 genomes]
rs34765154	0.85[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34871267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34878803	0.93[EUR][1000 genomes]
rs34950484	0.93[EUR][1000 genomes]
rs35001169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35016036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35017208	1.00[EUR][1000 genomes]
rs35030260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35072899	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35353359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35744819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35749575	0.85[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35883476	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36092177	0.96[EUR][1000 genomes]
rs55690788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56075693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56189111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67297533	0.82[EUR][1000 genomes]
rs67340775	0.94[EUR][1000 genomes]
rs67381177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67981811	0.96[EUR][1000 genomes]
rs67998226	0.93[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72854513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13214023	HLA-H	cis	multi-tissue	Pritchard
rs13214023	HLA-A	cis	multi-tissue	Pritchard
rs13214023	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13214023	ZFP57	cis	multi-tissue	Pritchard
rs13214023	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13214023	AL022393.7	cis	Muscle Skeletal	GTEx
rs13214023	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13214023	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
7	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
8	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
9	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:28324600-28332600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:28324600-28332600	Weak transcription	Brain Angular Gyrus	brain
14	chr6:28324600-28332600	Weak transcription	HSMM	muscle
15	chr6:28324600-28332800	Weak transcription	Fetal Heart	heart
16	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:28324600-28349600	Weak transcription	NHEK	skin
18	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:28325000-28332200	Weak transcription	HepG2	liver
21	chr6:28325000-28333200	Weak transcription	HMEC	breast
22	chr6:28325200-28333000	Weak transcription	Dnd41	blood
23	chr6:28325200-28333000	Weak transcription	NH-A	brain
24	chr6:28325400-28332800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:28325600-28333200	Weak transcription	HUVEC	blood vessel
27	chr6:28326800-28332800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28326800-28335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:28326800-28336200	Strong transcription	Adipose Nuclei	Adipose
30	chr6:28327000-28334800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:28327000-28334800	Strong transcription	Placenta	Placenta
32	chr6:28327000-28336200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:28327000-28336200	Strong transcription	Fetal Stomach	stomach
34	chr6:28327000-28337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:28327200-28334600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:28327200-28335400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr6:28327200-28338400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:28327400-28334200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:28327400-28334400	Strong transcription	Fetal Intestine Large	intestine
40	chr6:28327800-28335200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:28327800-28335600	Strong transcription	K562	blood
42	chr6:28328000-28333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:28328000-28334600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr6:28328000-28337000	Strong transcription	Liver	Liver
45	chr6:28328200-28334200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:28328200-28334400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:28328200-28334600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:28328200-28334600	Strong transcription	Osteobl	bone
49	chr6:28328200-28334800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:28328200-28334800	Strong transcription	Fetal Lung	lung

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