Variant report

Variant	rs2754248
Chromosome Location	chr6:88383880-88383881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88377817..88379372-chr6:88381342..88384204,2	K562	blood:
2	chr6:88382669..88387968-chr6:88408761..88414227,6	K562	blood:
3	chr6:88381197..88391198-chr6:88407466..88413401,14	K562	blood:
4	chr6:88377297..88379434-chr6:88381335..88385575,5	K562	blood:
5	chr6:88382184..88384921-chr6:88468055..88470522,2	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10755484	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13193380	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13194003	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246113	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2307379	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2325064	0.83[EUR][1000 genomes]
rs2754247	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2754260	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754264	0.80[EUR][1000 genomes]
rs2787893	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2787921	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2787924	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2787934	0.82[AMR][1000 genomes]
rs2814712	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757368	0.83[EUR][1000 genomes]
rs3934838	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334949	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4464759	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4498321	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587138	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4587143	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4706294	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707373	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4707374	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4707376	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707377	0.90[EUR][1000 genomes]
rs4707379	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707382	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707383	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6454632	0.86[EUR][1000 genomes]
rs6454636	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454638	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454640	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454641	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906769	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6908386	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916732	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6918909	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6928160	0.87[EUR][1000 genomes]
rs6930600	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6931069	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6940150	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7741825	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7742965	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7746465	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750207	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7752494	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7755167	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7757636	0.89[EUR][1000 genomes]
rs7757794	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762864	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7772561	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773906	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9444512	0.82[EUR][1000 genomes]
rs9444519	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444522	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9444524	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9444525	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444526	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444530	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450723	0.83[EUR][1000 genomes]
rs9450732	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450733	0.87[EUR][1000 genomes]
rs9450738	0.90[EUR][1000 genomes]
rs9450739	0.90[EUR][1000 genomes]
rs9450744	0.90[EUR][1000 genomes]
rs9450752	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9450755	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9450762	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2754248	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2754248	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2754248	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2754248	C6orf164	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
5	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
7	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
8	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:88324000-88385000	Weak transcription	Gastric	stomach
10	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
11	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
12	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:88349400-88397400	Weak transcription	Ovary	ovary
16	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
19	chr6:88364400-88384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:88367800-88385000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:88368000-88393400	Weak transcription	Small Intestine	intestine
25	chr6:88370200-88391800	Weak transcription	Fetal Brain Male	brain
26	chr6:88370400-88384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:88371600-88385000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:88372600-88392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:88374200-88391400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:88375600-88384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:88376200-88385800	Strong transcription	HSMM	muscle
32	chr6:88376400-88390000	Strong transcription	Primary B cells from cord blood	blood
33	chr6:88376600-88384800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:88376600-88390000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:88376800-88384600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:88376800-88389400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr6:88376800-88389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:88377200-88384800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:88377200-88388000	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:88377600-88384800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:88377600-88388000	Strong transcription	Placenta	Placenta
42	chr6:88378400-88384800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:88379000-88385600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:88379200-88384800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:88379400-88388400	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr6:88380400-88387600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:88380400-88387800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:88380400-88390000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:88380400-88391000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:88380600-88385000	Weak transcription	Spleen	Spleen

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