Variant report

Variant	rs2787924
Chromosome Location	chr6:88403429-88403430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88397239..88400435-chr6:88400607..88403655,3	K562	blood:
2	chr6:88389328..88391908-chr6:88402227..88405512,3	K562	blood:
3	chr6:88360758..88363835-chr6:88400530..88404540,3	K562	blood:
4	chr6:88394474..88397021-chr6:88403318..88405135,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10755484	0.84[EUR][1000 genomes]
rs13193380	0.89[EUR][1000 genomes]
rs13194003	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2246113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307379	0.94[EUR][1000 genomes]
rs2325064	0.82[EUR][1000 genomes]
rs2754247	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2754248	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2754260	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754262	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754264	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2787893	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2787921	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2787934	0.85[AMR][1000 genomes]
rs2814712	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3757368	0.82[EUR][1000 genomes]
rs3934838	0.89[EUR][1000 genomes]
rs4334949	0.90[EUR][1000 genomes]
rs4464759	0.89[EUR][1000 genomes]
rs4498321	0.93[EUR][1000 genomes]
rs4587138	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587143	0.90[EUR][1000 genomes]
rs4706294	0.93[EUR][1000 genomes]
rs4707373	0.83[EUR][1000 genomes]
rs4707374	0.88[EUR][1000 genomes]
rs4707376	0.90[EUR][1000 genomes]
rs4707377	0.90[EUR][1000 genomes]
rs4707379	0.90[EUR][1000 genomes]
rs4707382	0.93[EUR][1000 genomes]
rs4707383	0.93[EUR][1000 genomes]
rs6454632	0.85[EUR][1000 genomes]
rs6454636	0.93[EUR][1000 genomes]
rs6454638	0.93[EUR][1000 genomes]
rs6454640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6454641	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6906769	0.85[EUR][1000 genomes]
rs6908386	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6916732	0.88[EUR][1000 genomes]
rs6918909	0.83[EUR][1000 genomes]
rs6928160	0.87[EUR][1000 genomes]
rs6930600	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6931069	0.94[EUR][1000 genomes]
rs6940150	0.90[EUR][1000 genomes]
rs7742965	0.89[EUR][1000 genomes]
rs7746465	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7750207	0.90[EUR][1000 genomes]
rs7755167	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7757636	0.88[EUR][1000 genomes]
rs7757794	0.88[EUR][1000 genomes]
rs7762864	0.85[EUR][1000 genomes]
rs7772561	0.93[EUR][1000 genomes]
rs7773906	0.86[EUR][1000 genomes]
rs9444512	0.82[EUR][1000 genomes]
rs9444519	0.89[EUR][1000 genomes]
rs9444522	0.90[EUR][1000 genomes]
rs9444524	0.90[EUR][1000 genomes]
rs9444525	0.92[EUR][1000 genomes]
rs9444526	0.93[EUR][1000 genomes]
rs9450723	0.82[EUR][1000 genomes]
rs9450732	0.86[EUR][1000 genomes]
rs9450733	0.86[EUR][1000 genomes]
rs9450738	0.90[EUR][1000 genomes]
rs9450739	0.90[EUR][1000 genomes]
rs9450744	0.90[EUR][1000 genomes]
rs9450752	0.90[EUR][1000 genomes]
rs9450755	0.90[EUR][1000 genomes]
rs9450762	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2787924	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2787924	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2787924	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2787924	C6orf164	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
3	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
5	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:88392200-88405200	Weak transcription	Fetal Brain Male	brain
9	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
12	chr6:88392600-88406800	Weak transcription	HSMM	muscle
13	chr6:88392600-88407200	Weak transcription	HMEC	breast
14	chr6:88393600-88404000	Weak transcription	HUVEC	blood vessel
15	chr6:88393800-88405600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:88395000-88407200	Weak transcription	Hela-S3	cervix
17	chr6:88396400-88405200	Weak transcription	Stomach Mucosa	stomach
18	chr6:88397600-88407000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:88399000-88403800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:88399000-88407400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:88399600-88407400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:88399600-88408200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:88400000-88405600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:88400200-88406800	Weak transcription	NH-A	brain
25	chr6:88400400-88403600	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:88400400-88405400	Weak transcription	Dnd41	blood
27	chr6:88400800-88405600	Weak transcription	Gastric	stomach
28	chr6:88400800-88410000	Weak transcription	Lung	lung
29	chr6:88401000-88404400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:88401000-88408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:88401200-88406600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:88401600-88404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:88401600-88404400	Weak transcription	Brain Germinal Matrix	brain
34	chr6:88401800-88403600	Weak transcription	Fetal Heart	heart
35	chr6:88401800-88403800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:88401800-88404000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:88401800-88405200	Weak transcription	Fetal Intestine Large	intestine
38	chr6:88401800-88405600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:88401800-88406600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:88402000-88403800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:88402000-88404800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:88402000-88405000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:88402000-88405200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr6:88402000-88406800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:88402000-88406800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:88402000-88407400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:88402200-88403600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:88402200-88403600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:88402200-88403600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:88402200-88403600	Weak transcription	Colon Smooth Muscle	Colon

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