Variant report

Variant	rs6940744
Chromosome Location	chr6:28385957-28385958
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	chr6:28379842..28382776-chr6:28383800..28386316,2	K562	blood:
2	chr6:28385891..28388590-chr6:28390011..28392158,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1005126	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11751928	0.83[ASN][1000 genomes]
rs13190937	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13193272	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196606	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13199081	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203055	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13209596	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13215804	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13217326	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16894091	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894106	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232427	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28505234	0.83[ASN][1000 genomes]
rs3799499	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799500	0.83[ASN][1000 genomes]
rs57071502	0.83[ASN][1000 genomes]
rs58020991	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6902687	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6905380	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6931359	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71559081	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740429	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7750526	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7754960	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7774981	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468356	0.83[ASN][1000 genomes]
rs9468358	0.83[ASN][1000 genomes]
rs9969098	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs6940744	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6940744	ZSCAN23	cis	Artery Tibial	GTEx
rs6940744	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs6940744	AL022393.7	cis	Muscle Skeletal	GTEx
rs6940744	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs6940744	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28377000-28386600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28377600-28390200	Weak transcription	Fetal Lung	lung
4	chr6:28379400-28389200	Weak transcription	HSMM	muscle
5	chr6:28380800-28390600	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:28381400-28390000	Weak transcription	Fetal Brain Female	brain
7	chr6:28382600-28386600	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:28382800-28387600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:28383400-28390600	Weak transcription	Fetal Stomach	stomach
10	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
11	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:28384000-28386600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28384000-28387600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:28384200-28386800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:28384600-28386800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:28384600-28387800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:28384600-28390200	Weak transcription	NH-A	brain
18	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:28384800-28388000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:28384800-28388400	Weak transcription	Small Intestine	intestine
21	chr6:28384800-28390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:28385000-28387400	Weak transcription	NHDF-Ad	bronchial
23	chr6:28385000-28390600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:28385200-28390600	Weak transcription	Placenta	Placenta
25	chr6:28385400-28391000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:28385400-28391200	Weak transcription	HSMMtube	muscle
27	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
28	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:28385600-28390800	Weak transcription	Aorta	Aorta
30	chr6:28385600-28390800	Weak transcription	Ovary	ovary
31	chr6:28385600-28410800	Weak transcription	Lung	lung
32	chr6:28385800-28387600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:28385800-28390800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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