Variant report

Variant	rs2754264
Chromosome Location	chr6:88406877-88406878
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88406148..88410116-chr6:88433158..88435018,3	K562	blood:
2	chr6:88355100..88357756-chr6:88404547..88407101,2	K562	blood:
3	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:
4	chr6:88391827..88396132-chr6:88405533..88410317,6	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2246113	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2307379	0.80[EUR][1000 genomes]
rs2754247	0.81[EUR][1000 genomes]
rs2754248	0.80[EUR][1000 genomes]
rs2754260	0.83[EUR][1000 genomes]
rs2754262	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787893	0.82[EUR][1000 genomes]
rs2787921	0.83[EUR][1000 genomes]
rs2787924	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814712	0.84[EUR][1000 genomes]
rs6454640	0.81[EUR][1000 genomes]
rs6454641	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv7941	chr6:88403555-88413595	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2754264	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2754264	C6orf164	cis	Thyroid	GTEx
rs2754264	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2754264	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
8	chr6:88392600-88407200	Weak transcription	HMEC	breast
9	chr6:88395000-88407200	Weak transcription	Hela-S3	cervix
10	chr6:88397600-88407000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:88399000-88407400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:88399600-88407400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:88399600-88408200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:88400800-88410000	Weak transcription	Lung	lung
15	chr6:88401000-88408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:88402000-88407400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:88402200-88407200	Weak transcription	K562	blood
18	chr6:88402200-88407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:88402200-88407800	Weak transcription	Placenta	Placenta
20	chr6:88402200-88410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:88402600-88407200	Enhancers	Adipose Nuclei	Adipose
22	chr6:88402800-88407200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:88403200-88407800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:88403200-88408200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:88403400-88407200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:88403400-88407400	Enhancers	Liver	Liver
27	chr6:88403400-88407800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr6:88403400-88410000	Weak transcription	Esophagus	oesophagus
29	chr6:88403600-88408400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:88403800-88407200	Enhancers	HepG2	liver
31	chr6:88404000-88407600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:88404200-88407000	Weak transcription	NHDF-Ad	bronchial
33	chr6:88404200-88407200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:88404800-88407400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:88405000-88407200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:88405200-88407200	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:88405200-88407200	Enhancers	Fetal Brain Male	brain
38	chr6:88405200-88407200	Enhancers	Osteobl	bone
39	chr6:88405200-88408200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:88405400-88407000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr6:88405400-88407400	Enhancers	Primary B cells from cord blood	blood
42	chr6:88405600-88407000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:88405600-88407000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:88405600-88407000	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:88405600-88407200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:88405600-88407200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:88405600-88407400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:88405600-88407800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:88405600-88408000	Enhancers	Left Ventricle	heart
50	chr6:88405800-88407000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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