Variant report

Variant	rs13211507
Chromosome Location	chr6:28257377-28257378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28255421..28258446-chr6:28262353..28265432,3	K562	blood:
2	chr6:28246849..28251135-chr6:28253254..28258623,13	K562	blood:
3	chr6:28255210..28257728-chr6:28316331..28318308,2	K562	blood:
4	chr6:28184805..28186411-chr6:28255755..28258597,2	K562	blood:
5	chr6:28255681..28258623-chr6:28265550..28268633,3	K562	blood:

Variant related genes	Relation type
ENSG00000189298	Chromatin interaction
ENSG00000137338	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs13190888	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13191038	0.85[EUR][1000 genomes]
rs13191786	1.00[EUR][1000 genomes]
rs13195291	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13197574	0.85[EUR][1000 genomes]
rs13197633	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13198809	0.93[EUR][1000 genomes]
rs13201308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13201681	0.93[EUR][1000 genomes]
rs13203816	0.85[EUR][1000 genomes]
rs13204012	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13205211	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13205911	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs13207345	1.00[EUR][1000 genomes]
rs13208096	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13213152	0.83[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13213986	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs13214023	1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13217619	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13217984	0.85[EUR][1000 genomes]
rs2232423	0.83[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232426	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232429	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33932084	0.98[EUR][1000 genomes]
rs34166054	0.85[EUR][1000 genomes]
rs34218844	1.00[EUR][1000 genomes]
rs34243448	1.00[EUR][1000 genomes]
rs34371502	0.85[EUR][1000 genomes]
rs34396849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34505829	0.85[EUR][1000 genomes]
rs34546986	0.89[EUR][1000 genomes]
rs34588114	0.85[EUR][1000 genomes]
rs34661125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34676049	0.93[EUR][1000 genomes]
rs34691223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34765154	0.85[EUR][1000 genomes]
rs34832585	0.85[EUR][1000 genomes]
rs34871267	0.89[EUR][1000 genomes]
rs34878803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34950484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35001169	0.93[EUR][1000 genomes]
rs35016036	0.96[EUR][1000 genomes]
rs35017208	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35030260	0.98[EUR][1000 genomes]
rs35072899	1.00[EUR][1000 genomes]
rs35098436	0.85[EUR][1000 genomes]
rs35345226	0.85[EUR][1000 genomes]
rs35353359	0.93[EUR][1000 genomes]
rs35656932	0.93[EUR][1000 genomes]
rs35744819	0.93[EUR][1000 genomes]
rs35749575	0.85[EUR][1000 genomes]
rs35781323	0.85[EUR][1000 genomes]
rs35883476	0.89[EUR][1000 genomes]
rs35902873	0.85[EUR][1000 genomes]
rs36092177	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55690788	0.93[EUR][1000 genomes]
rs56075693	1.00[EUR][1000 genomes]
rs56189111	1.00[EUR][1000 genomes]
rs66886492	0.85[EUR][1000 genomes]
rs67297533	0.82[EUR][1000 genomes]
rs67340775	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67381177	0.93[EUR][1000 genomes]
rs67981811	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67998226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559070	0.85[EUR][1000 genomes]
rs71559072	0.85[EUR][1000 genomes]
rs72846780	0.85[EUR][1000 genomes]
rs72846794	0.85[EUR][1000 genomes]
rs72854513	1.00[EUR][1000 genomes]
rs7752448	0.90[CEU][hapmap]
rs7752608	0.81[EUR][1000 genomes]
rs7767244	1.00[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13211507	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13211507	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13211507	AL022393.7	cis	Muscle Skeletal	GTEx
rs13211507	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28258000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:28250000-28258600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:28250000-28293800	Weak transcription	Gastric	stomach
6	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
7	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:28250600-28267000	Weak transcription	NHEK	skin
10	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
11	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:28250800-28257600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
14	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:28251000-28258200	Strong transcription	Fetal Muscle Leg	muscle
16	chr6:28251000-28258600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:28251000-28258600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
19	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:28251200-28257600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:28251200-28258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:28251200-28258400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:28251200-28259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:28251200-28259400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:28251400-28257400	Strong transcription	Adipose Nuclei	Adipose
28	chr6:28251400-28258000	Strong transcription	Fetal Brain Female	brain
29	chr6:28251400-28262200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:28251600-28257600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:28251600-28258200	Strong transcription	Colon Smooth Muscle	Colon
32	chr6:28251600-28258200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr6:28251600-28258400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:28251600-28258400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:28251600-28258400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:28251600-28258400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:28251800-28257600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:28251800-28257600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28251800-28257600	Strong transcription	Brain Angular Gyrus	brain
40	chr6:28251800-28257600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:28251800-28257800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:28251800-28258000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:28251800-28258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:28252000-28258000	Strong transcription	NH-A	brain
45	chr6:28252000-28258600	Strong transcription	Brain Germinal Matrix	brain
46	chr6:28252200-28258000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:28252400-28258000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:28252400-28258200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:28252400-28259000	Strong transcription	HSMM	muscle
50	chr6:28252400-28259400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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