Variant report

Variant	rs13209596
Chromosome Location	chr6:28396190-28396191
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28390398..28392930-chr6:28395199..28398373,4	K562	blood:
2	chr6:28389572..28392930-chr6:28395042..28397704,3	K562	blood:
3	chr6:28373846..28375488-chr6:28394522..28397398,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005126	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807030	0.82[ASN][1000 genomes]
rs10807031	0.82[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11755387	0.88[CHB][hapmap]
rs13190937	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13193272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196606	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199081	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs13203055	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215804	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13217326	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16894011	0.86[CHB][hapmap]
rs16894091	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894106	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17856167	0.88[CHB][hapmap]
rs2021745	0.88[YRI][hapmap]
rs2108923	0.82[ASN][1000 genomes]
rs2232427	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531813	0.84[YRI][hapmap]
rs28505234	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2859372	0.84[YRI][hapmap]
rs2859373	0.85[YRI][hapmap]
rs2859374	0.84[YRI][hapmap]
rs35908902	0.82[ASN][1000 genomes]
rs3799499	0.89[CEU][hapmap];0.84[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57071502	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58020991	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6905380	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6931359	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940744	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71559081	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740429	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750526	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754960	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774981	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468356	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9468364	0.86[CHB][hapmap]
rs9969098	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13209596	AL022393.7	cis	Muscle Skeletal	GTEx
rs13209596	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13209596	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13209596	ZSCAN23	cis	Artery Tibial	GTEx
rs13209596	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs13209596	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
4	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:28385600-28410800	Weak transcription	Lung	lung
6	chr6:28386000-28402200	Weak transcription	Osteobl	bone
7	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
11	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
12	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:28389200-28410200	Weak transcription	NHLF	lung
14	chr6:28389400-28403200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:28389600-28398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
22	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:28391400-28402400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:28391400-28410400	Weak transcription	Fetal Intestine Large	intestine
25	chr6:28391400-28410800	Weak transcription	Placenta	Placenta
26	chr6:28391600-28397600	Weak transcription	Ovary	ovary
27	chr6:28391600-28401800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:28391600-28402000	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:28391600-28402000	Weak transcription	Left Ventricle	heart
30	chr6:28391600-28402000	Weak transcription	Psoas Muscle	Psoas
31	chr6:28391600-28402200	Weak transcription	HSMMtube	muscle
32	chr6:28391600-28402200	Weak transcription	NH-A	brain
33	chr6:28391600-28410200	Weak transcription	Brain Anterior Caudate	brain
34	chr6:28391600-28410800	Weak transcription	Pancreas	Pancrea
35	chr6:28392000-28397800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:28392000-28398200	Weak transcription	HSMM	muscle
37	chr6:28392000-28410200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:28392000-28410400	Weak transcription	NHEK	skin
39	chr6:28392200-28402000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:28392200-28410400	Weak transcription	Right Ventricle	heart
41	chr6:28392400-28397800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:28392400-28410000	Weak transcription	HMEC	breast
43	chr6:28392400-28410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:28393400-28397200	Weak transcription	Fetal Stomach	stomach
45	chr6:28393600-28397000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:28393600-28410800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:28393800-28396600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:28393800-28402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:28393800-28404200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:28393800-28410600	Weak transcription	Aorta	Aorta

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