Variant report

Variant	rs2754260
Chromosome Location	chr6:88397666-88397667
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	chr6:88389146..88392060-chr6:88395023..88397672,4	K562	blood:
3	chr6:88384987..88388432-chr6:88394955..88398882,4	K562	blood:
4	chr6:88384987..88386595-chr6:88394955..88397746,2	K562	blood:
5	chr6:88397124..88399437-chr6:88612572..88615497,2	K562	blood:
6	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:
7	chr6:88389765..88392894-chr6:88395067..88397964,5	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10755484	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13193380	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13194003	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246113	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2307379	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2325064	0.82[EUR][1000 genomes]
rs2754247	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754248	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754262	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2754264	0.83[EUR][1000 genomes]
rs2787893	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2787921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787924	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2787934	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2814712	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757368	0.82[EUR][1000 genomes]
rs3934838	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4464759	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4498321	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4587138	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4587143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4706294	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707373	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707374	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707376	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707377	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707379	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707382	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707383	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6454632	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6454636	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454638	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454640	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454641	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906769	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6908386	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6916732	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6918909	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6928160	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6930600	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6931069	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6940150	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7741825	0.83[ASN][1000 genomes]
rs7742965	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7746465	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7750207	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7752494	0.82[ASN][1000 genomes]
rs7755167	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757636	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7757794	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762864	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7772561	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773906	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444512	0.82[EUR][1000 genomes]
rs9444519	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444522	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444524	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444525	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444526	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444530	0.84[ASN][1000 genomes]
rs9450723	0.82[EUR][1000 genomes]
rs9450732	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450733	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450738	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450739	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450744	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450752	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450755	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450762	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2754260	SLC35A1	cis	multi-tissue	Pritchard
rs2754260	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2754260	C6orf164	cis	Thyroid	GTEx
rs2754260	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2754260	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
6	chr6:88385400-88399800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
8	chr6:88385800-88398600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:88385800-88399200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:88386200-88399000	Weak transcription	Gastric	stomach
11	chr6:88387400-88398600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
13	chr6:88387800-88400600	Weak transcription	K562	blood
14	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
15	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
17	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
18	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:88390400-88398800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:88390400-88399600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:88390400-88400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
23	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain
31	chr6:88391400-88400800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:88391600-88399400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:88391800-88399600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:88392000-88399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:88392000-88399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:88392000-88400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:88392000-88401200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:88392200-88400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:88392200-88405200	Weak transcription	Fetal Brain Male	brain
40	chr6:88392400-88400600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:88392400-88400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:88392400-88401400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
46	chr6:88392600-88398400	Weak transcription	NH-A	brain
47	chr6:88392600-88399800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:88392600-88406800	Weak transcription	HSMM	muscle
49	chr6:88392600-88407200	Weak transcription	HMEC	breast
50	chr6:88393000-88400000	Weak transcription	Osteobl	bone

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