Variant report

Variant	rs6744560
Chromosome Location	chr2:37130658-37130659
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37119952..37122407-chr2:37130124..37132171,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17020071	0.82[YRI][hapmap]
rs17332671	1.00[CHB][hapmap]
rs17404648	1.00[CHB][hapmap]
rs17496249	0.80[AFR][1000 genomes]
rs17497197	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2110942	0.80[AFR][1000 genomes]
rs2247010	1.00[CHB][hapmap]
rs6716891	1.00[CHB][hapmap]
rs7560263	0.83[AFR][1000 genomes]
rs888083	0.82[ASW][hapmap];0.84[LWK][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6744560	Contig34947_RC	cis	multi-tissue	Pritchard
rs6744560	EIF2AK2	cis	cerebellum	SCAN
rs6744560	ATL2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37067600-37146200	Weak transcription	Psoas Muscle	Psoas
2	chr2:37075600-37139200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:37077200-37144400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:37077400-37136600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:37087400-37146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:37094400-37154200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:37096400-37143800	Weak transcription	Fetal Kidney	kidney
8	chr2:37096800-37154400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:37099200-37140200	Weak transcription	Colonic Mucosa	Colon
10	chr2:37103800-37146200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:37105000-37152600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:37105000-37164600	Weak transcription	Lung	lung
13	chr2:37105200-37136200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:37105200-37139200	Weak transcription	Aorta	Aorta
15	chr2:37105200-37141200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:37105200-37144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:37105200-37154400	Weak transcription	Esophagus	oesophagus
18	chr2:37105200-37157800	Weak transcription	Pancreas	Pancrea
19	chr2:37105200-37164600	Weak transcription	Spleen	Spleen
20	chr2:37105800-37146400	Weak transcription	Right Ventricle	heart
21	chr2:37110000-37135800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:37110800-37142800	Weak transcription	Gastric	stomach
23	chr2:37111200-37140600	Weak transcription	Fetal Brain Female	brain
24	chr2:37111600-37139200	Weak transcription	Ovary	ovary
25	chr2:37111800-37138200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:37112000-37138400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:37112400-37145800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:37114000-37145800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:37116200-37131400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:37117400-37139400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:37117400-37144400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:37117600-37131000	Weak transcription	NH-A	brain
33	chr2:37117600-37139800	Weak transcription	HSMM	muscle
34	chr2:37117600-37153600	Weak transcription	Hela-S3	cervix
35	chr2:37118000-37139200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:37118000-37139600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:37118000-37139800	Weak transcription	HUVEC	blood vessel
38	chr2:37118000-37140000	Weak transcription	NHEK	skin
39	chr2:37118000-37140200	Weak transcription	HMEC	breast
40	chr2:37118200-37139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:37118200-37139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:37118800-37131600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:37119600-37139000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:37119600-37139200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:37119600-37139200	Weak transcription	Osteobl	bone
46	chr2:37119600-37140000	Weak transcription	GM12878-XiMat	blood
47	chr2:37119800-37142200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:37120000-37139200	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:37120000-37139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:37120000-37153800	Weak transcription	Stomach Smooth Muscle	stomach

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