Variant report

Variant	rs2938319
Chromosome Location	chr1:114525636-114525637
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114524706..114527224-chr1:114758079..114759790,2	MCF-7	breast:
2	chr1:114525379..114527622-chr1:114550008..114552290,2	MCF-7	breast:
3	chr1:114524848..114527263-chr1:114536709..114538580,2	MCF-7	breast:
4	chr1:114524656..114527176-chr1:114534209..114536962,2	K562	blood:
5	chr1:114524538..114527431-chr1:114576171..114578316,2	MCF-7	breast:
6	chr1:114523957..114526156-chr16:67217978..67219734,2	MCF-7	breast:
7	chr1:114524519..114527329-chr1:114827145..114829580,2	MCF-7	breast:
8	chr1:114523401..114526223-chr1:114556190..114558490,2	MCF-7	breast:
9	chr1:114519994..114522230-chr1:114524239..114526511,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116774	Chromatin interaction
ENSG00000179044	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11102704	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs11102712	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1158910	0.88[ASN][1000 genomes]
rs1158911	0.89[ASN][1000 genomes]
rs1158912	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12029644	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12029840	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1354373	0.89[ASN][1000 genomes]
rs17032048	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806763	0.91[ASN][1000 genomes]
rs2358997	0.81[ASN][1000 genomes]
rs2358998	0.83[ASN][1000 genomes]
rs2884604	0.83[ASN][1000 genomes]
rs2938320	0.87[ASN][1000 genomes]
rs3006981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006988	0.89[ASN][1000 genomes]
rs3006989	0.89[ASN][1000 genomes]
rs3006996	0.90[ASN][1000 genomes]
rs3006998	0.87[ASN][1000 genomes]
rs3006999	0.87[ASN][1000 genomes]
rs3007002	0.86[ASN][1000 genomes]
rs7520320	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs924778	0.92[ASN][1000 genomes]
rs937672	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2938319	SYT6	cis	parietal	SCAN
rs2938319	OVGP1	cis	cerebellum	SCAN
rs2938319	PTPN22	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114518800-114525800	Weak transcription	Esophagus	oesophagus
2	chr1:114519800-114527000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:114521600-114526600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr1:114521600-114527000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:114522200-114526000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:114522200-114526200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:114522400-114527400	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr1:114522800-114526200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:114523000-114526200	Weak transcription	Fetal Brain Female	brain
10	chr1:114523000-114526400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:114523000-114526600	Weak transcription	HUVEC	blood vessel
12	chr1:114523200-114526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:114523400-114527200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:114523800-114526600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:114523800-114526600	Flanking Active TSS	HSMM	muscle
16	chr1:114523800-114534600	Weak transcription	Primary T cells from cord blood	blood
17	chr1:114524000-114526400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:114524000-114527800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:114524200-114526400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:114524200-114526600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:114524200-114526600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:114524400-114525800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:114524400-114526200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:114524400-114526400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:114524400-114526800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:114524400-114527000	Flanking Active TSS	Fetal Lung	lung
27	chr1:114524400-114528000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:114524600-114526000	Enhancers	NH-A	brain
29	chr1:114524600-114526000	Flanking Active TSS	NHDF-Ad	bronchial
30	chr1:114524600-114526000	Flanking Active TSS	Osteobl	bone
31	chr1:114524600-114526200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:114524600-114526400	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr1:114524600-114526600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:114524600-114526600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr1:114524600-114526600	Enhancers	Fetal Heart	heart
36	chr1:114524600-114526600	Enhancers	Pancreas	Pancrea
37	chr1:114524600-114526800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr1:114524800-114526000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:114524800-114526800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:114524800-114527600	Enhancers	Fetal Thymus	thymus
41	chr1:114524800-114528000	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr1:114525000-114525800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:114525000-114525800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:114525000-114525800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr1:114525000-114525800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:114525000-114526000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:114525000-114526000	Active TSS	Colon Smooth Muscle	Colon
48	chr1:114525000-114526000	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr1:114525000-114526000	Flanking Active TSS	NHLF	lung
50	chr1:114525000-114526200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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