Variant report

Variant	rs240785
Chromosome Location	chr6:100973377-100973378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11964230	0.89[AMR][1000 genomes]
rs17054273	0.89[AMR][1000 genomes]
rs171257	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs183023	1.00[AMR][1000 genomes]
rs2201495	0.89[AMR][1000 genomes]
rs239192	1.00[AMR][1000 genomes]
rs239200	1.00[AMR][1000 genomes]
rs239205	1.00[AMR][1000 genomes]
rs239214	1.00[AMR][1000 genomes]
rs239224	1.00[AMR][1000 genomes]
rs239233	1.00[AMR][1000 genomes]
rs239243	1.00[AMR][1000 genomes]
rs239244	1.00[AMR][1000 genomes]
rs2398133	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240122	1.00[AMR][1000 genomes]
rs240144	1.00[AMR][1000 genomes]
rs240155	1.00[AMR][1000 genomes]
rs240157	1.00[AMR][1000 genomes]
rs240165	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240166	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs240768	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs240777	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240779	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs240782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3213542	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs33988845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs401864	0.80[CEU][hapmap]
rs412177	1.00[AMR][1000 genomes]
rs4240588	1.00[AMR][1000 genomes]
rs6927313	0.89[AMR][1000 genomes]
rs6931919	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72939355	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72941252	0.94[AMR][1000 genomes]
rs72942932	0.89[AMR][1000 genomes]
rs72942985	0.89[AMR][1000 genomes]
rs72949504	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9373580	1.00[AMR][1000 genomes]
rs9689068	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs240785	CCNC	cis	lymphoblastoid	seeQTL
rs240785	GRIK2	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100952800-100997400	Weak transcription	A549	lung
2	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
3	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
5	chr6:100958200-100976600	Weak transcription	NHDF-Ad	bronchial
6	chr6:100958600-100974000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:100960200-100978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:100960600-100973800	Weak transcription	HUVEC	blood vessel
9	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:100960800-100974000	Weak transcription	NH-A	brain
11	chr6:100960800-100977600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:100960800-100981000	Weak transcription	Gastric	stomach
13	chr6:100960800-100986000	Weak transcription	GM12878-XiMat	blood
14	chr6:100960800-100986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:100960800-100986600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:100960800-100989600	Weak transcription	K562	blood
17	chr6:100960800-100989800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:100961000-100986600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:100961000-100987200	Weak transcription	Osteobl	bone
21	chr6:100961000-100988800	Weak transcription	NHEK	skin
22	chr6:100961000-100991200	Weak transcription	HSMMtube	muscle
23	chr6:100961000-100992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:100961000-100997200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:100961200-100989000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:100961400-100986000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:100963000-100986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:100964000-100990800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:100964200-100986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:100964200-101020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:100964800-100998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:100965200-100984000	Weak transcription	HepG2	liver
33	chr6:100965200-100986600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:100965200-100989600	Weak transcription	Aorta	Aorta
35	chr6:100965200-100990200	Weak transcription	Left Ventricle	heart
36	chr6:100965200-101000800	Weak transcription	Fetal Intestine Small	intestine
37	chr6:100965200-101011400	Weak transcription	Pancreas	Pancrea
38	chr6:100965400-100976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:100965400-100976600	Weak transcription	HSMM	muscle
40	chr6:100965400-100977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:100965400-100984200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr6:100965400-100984400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:100965400-100984400	Weak transcription	Psoas Muscle	Psoas
44	chr6:100965400-100985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:100965400-100986600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:100965400-100988600	Weak transcription	Lung	lung
47	chr6:100965400-100989600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:100965400-100989800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:100965400-100990400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:100965400-100991800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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