Variant report

Variant	rs2754245
Chromosome Location	chr6:88382859-88382860
allele	A/G
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	chr6:88365678..88369337-chr6:88379834..88383154,3	K562	blood:
5	chr6:88377297..88379434-chr6:88381335..88385575,5	K562	blood:
6	chr6:88382184..88384921-chr6:88468055..88470522,2	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1051131	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1051148	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs10755484	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs2246113	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs2268993	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2268994	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2284908	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2300906	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2300909	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2754247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2754262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap]
rs2787893	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2787927	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs2814712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs3757368	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs3934838	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4334949	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs4464759	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs4587138	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4587143	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6454631	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6916732	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7741825	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7761814	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7773906	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9444519	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9444522	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9450712	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9450723	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs9450732	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9450752	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs985764	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2754245	SLC35A1	cis	parietal	SCAN
rs2754245	C6orf164	cis	Thyroid	GTEx
rs2754245	SLC35A1	cis	multi-tissue	Pritchard
rs2754245	SNORD50A	cis	cerebellum	SCAN
rs2754245	SLC35A1	cis	lymphoblastoid	seeQTL
rs2754245	C6orf162	cis	cerebellum	SCAN
rs2754245	C6orf162	cis	parietal	SCAN
rs2754245	GJB7	cis	cerebellum	SCAN

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	chr6:88329800-88383200	Weak transcription	Lung	lung
11	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
13	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:88349400-88397400	Weak transcription	Ovary	ovary
17	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
20	chr6:88364400-88384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:88367800-88385000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:88368000-88393400	Weak transcription	Small Intestine	intestine
26	chr6:88370200-88391800	Weak transcription	Fetal Brain Male	brain
27	chr6:88370400-88384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:88371000-88383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:88371600-88383400	Weak transcription	Psoas Muscle	Psoas
30	chr6:88371600-88385000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:88372600-88392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:88372800-88383000	Weak transcription	Fetal Stomach	stomach
33	chr6:88374200-88391400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:88375600-88384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:88376200-88385800	Strong transcription	HSMM	muscle
36	chr6:88376400-88390000	Strong transcription	Primary B cells from cord blood	blood
37	chr6:88376600-88384800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:88376600-88390000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:88376800-88384600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:88376800-88389400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:88376800-88389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:88377000-88383200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:88377200-88384800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:88377200-88388000	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:88377600-88384800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:88377600-88388000	Strong transcription	Placenta	Placenta
47	chr6:88377800-88383200	Strong transcription	Osteobl	bone
48	chr6:88378400-88383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:88378400-88384800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:88379000-88385600	Strong transcription	Primary B cells from peripheral blood	blood

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