Variant report

Variant	rs1713979
Chromosome Location	chr4:57943749-57943750
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57943158..57945422-chr4:57946459..57948764,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10009533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573051	1.00[JPT][hapmap]
rs11573053	0.87[ASN][1000 genomes]
rs11573063	1.00[JPT][hapmap]
rs11573079	0.82[JPT][hapmap]
rs11934877	1.00[JPT][hapmap]
rs1522609	0.81[CEU][hapmap]
rs1620509	0.82[CEU][hapmap]
rs1713976	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1713977	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1713980	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1713981	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714004	0.81[CEU][hapmap]
rs1714010	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1714011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714012	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718844	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718845	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1718846	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718847	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718851	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1718861	0.81[CEU][hapmap]
rs4864611	0.82[JPT][hapmap]
rs4865174	0.82[JPT][hapmap]
rs9997862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1713979	KIT	cis	cerebellum	SCAN
rs1713979	POLR2B	cis	parietal	SCAN
rs1713979	IGFBP7	cis	parietal	SCAN
rs1713979	FIP1L1	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57929600-57944400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:57932400-57945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:57932400-57947600	Genic enhancers	Osteobl	bone
4	chr4:57932600-57944000	Weak transcription	Fetal Stomach	stomach
5	chr4:57934400-57951600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:57934600-57948200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:57935600-57944000	Weak transcription	Fetal Thymus	thymus
8	chr4:57935800-57945000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:57935800-57948000	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:57936200-57945000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:57937400-57948000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:57937600-57944200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:57937800-57943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:57937800-57944000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:57937800-57945000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:57937800-57946800	Weak transcription	Adipose Nuclei	Adipose
17	chr4:57938000-57945600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:57938000-57955800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:57938800-57947000	Weak transcription	Esophagus	oesophagus
20	chr4:57939800-57944200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:57939800-57949800	Enhancers	HMEC	breast
22	chr4:57940000-57946200	Weak transcription	Lung	lung
23	chr4:57940200-57943800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:57940400-57943800	Weak transcription	Spleen	Spleen
25	chr4:57940800-57944200	Enhancers	A549	lung
26	chr4:57941200-57943800	Weak transcription	HSMM	muscle
27	chr4:57941200-57944000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr4:57941200-57944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:57941200-57944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:57941200-57944800	Weak transcription	Ovary	ovary
31	chr4:57941200-57945000	Weak transcription	Small Intestine	intestine
32	chr4:57941400-57944400	Weak transcription	Fetal Intestine Small	intestine
33	chr4:57941400-57947000	Weak transcription	Brain Substantia Nigra	brain
34	chr4:57941800-57943800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:57941800-57943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:57941800-57943800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:57941800-57944600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:57941800-57945000	Weak transcription	Fetal Intestine Large	intestine
39	chr4:57942000-57944000	Strong transcription	HSMMtube	muscle
40	chr4:57942000-57945200	Weak transcription	Hela-S3	cervix
41	chr4:57942000-57947000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:57942000-57947800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:57942200-57943800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:57942200-57943800	Weak transcription	NHLF	lung
45	chr4:57942200-57944000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:57942200-57945000	Weak transcription	NHDF-Ad	bronchial
47	chr4:57942200-57946600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:57942400-57945000	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:57942600-57943800	Weak transcription	Right Ventricle	heart
50	chr4:57942600-57945600	Weak transcription	Primary hematopoietic stem cells	blood

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