Variant report

Variant	rs2857781
Chromosome Location	chr6:29628740-29628741
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1233373	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1233375	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1233378	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12661228	0.95[EUR][1000 genomes]
rs12661266	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1318631	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17184549	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17369215	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17435027	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs17875376	0.84[EUR][1000 genomes]
rs2252711	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2256266	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2857766	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34387568	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34912326	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35471702	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4084764	0.84[EUR][1000 genomes]
rs4391284	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713230	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4713232	0.89[AFR][1000 genomes]
rs4713233	0.93[EUR][1000 genomes]
rs4713237	0.82[EUR][1000 genomes]
rs4713239	0.82[EUR][1000 genomes]
rs4713240	0.82[EUR][1000 genomes]
rs4959123	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7754067	0.84[EUR][1000 genomes]
rs9368609	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2857781	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
3	chr6:29620000-29628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain
6	chr6:29624400-29629200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:29624400-29630400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:29624800-29628800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:29624800-29629000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:29624800-29631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:29625000-29628800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:29625000-29628800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:29625000-29628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:29625000-29629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:29625000-29629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
17	chr6:29625200-29628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:29625200-29628800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:29626600-29631400	Weak transcription	Fetal Heart	heart
20	chr6:29627800-29629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:29628000-29628800	Weak transcription	Brain Angular Gyrus	brain
22	chr6:29628000-29628800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:29628000-29628800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:29628000-29630200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:29628400-29630200	Active TSS	Brain Hippocampus Middle	brain
26	chr6:29628600-29629000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:29628600-29631800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:29628600-29632000	Enhancers	HUES48 Cell Line	embryonic stem cell

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