Variant report

Variant	rs2760138
Chromosome Location	chr6:24512837-24512838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1569579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2010190	0.83[CHB][hapmap]
rs2744572	0.83[CHB][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2744582	0.83[AMR][1000 genomes]
rs2744588	0.82[EUR][1000 genomes]
rs2744593	0.82[AMR][1000 genomes]
rs2744597	0.81[MEX][hapmap]
rs2760137	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2760146	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2760153	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2817226	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2817229	0.83[ASN][1000 genomes]
rs807512	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs807513	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs807515	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs807518	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2760138	HIST1H4C	cis	parietal	SCAN
rs2760138	HIST1H2BC	cis	cerebellum	SCAN
rs2760138	SLC17A2	cis	parietal	SCAN
rs2760138	HIST1H1E	cis	cerebellum	SCAN
rs2760138	ABT1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24495800-24517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:24496000-24513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24496000-24517800	Weak transcription	Spleen	Spleen
4	chr6:24496000-24534200	Weak transcription	Gastric	stomach
5	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
6	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
7	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
11	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
12	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
14	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:24496800-24522800	Weak transcription	Lung	lung
16	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:24497000-24528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:24497400-24522400	Weak transcription	K562	blood
19	chr6:24498400-24517400	Weak transcription	GM12878-XiMat	blood
20	chr6:24498800-24517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:24504200-24513800	Weak transcription	Aorta	Aorta
22	chr6:24504200-24522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
24	chr6:24505200-24516800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:24505600-24516000	Weak transcription	A549	lung
27	chr6:24505800-24513400	Weak transcription	Left Ventricle	heart
28	chr6:24505800-24527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:24505800-24530800	Weak transcription	Right Ventricle	heart
30	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:24506200-24513000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:24506400-24513800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:24506400-24514000	Weak transcription	Ovary	ovary
35	chr6:24506400-24530000	Weak transcription	Placenta	Placenta
36	chr6:24506800-24518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:24507400-24513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:24507400-24513800	Weak transcription	Fetal Intestine Large	intestine
39	chr6:24507400-24531400	Weak transcription	Fetal Lung	lung
40	chr6:24507600-24514000	Weak transcription	Brain Angular Gyrus	brain
41	chr6:24507600-24514200	Weak transcription	Brain Anterior Caudate	brain
42	chr6:24507600-24522800	Weak transcription	Fetal Kidney	kidney
43	chr6:24507600-24532400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:24507600-24532400	Weak transcription	Fetal Brain Female	brain
45	chr6:24507800-24513200	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:24507800-24513800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:24507800-24532400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:24507800-24536800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:24507800-24539200	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:24508000-24515400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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