Variant report

Variant	rs3737142
Chromosome Location	chr9:97933252-97933253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97910896..97912573-chr9:97931774..97933333,2	K562	blood:
2	chr9:97904743..97906856-chr9:97933205..97935639,2	MCF-7	breast:
3	chr9:97928874..97931668-chr9:97931897..97933841,2	K562	blood:

Variant related genes	Relation type
ENSG00000251884	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10115247	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011784	0.91[JPT][hapmap]
rs10739992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739993	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761374	0.86[JPT][hapmap]
rs10761377	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10761382	0.88[CEU][hapmap]
rs10821447	0.91[JPT][hapmap]
rs10821451	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821454	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993490	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13295862	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17686583	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2166402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282216	0.96[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297596	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404457	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34045846	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34532504	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3780561	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3780562	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3780564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780567	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3824486	0.88[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs3844341	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647443	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4647462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4647528	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647529	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647534	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647554	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647558	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4657	0.91[JPT][hapmap]
rs4743988	0.91[JPT][hapmap]
rs4744442	0.91[JPT][hapmap]
rs4744446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744451	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744454	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479601	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019043	0.86[EUR][1000 genomes]
rs7023007	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7034538	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7042293	0.81[JPT][hapmap]
rs7042320	0.82[JPT][hapmap]
rs7046682	0.91[JPT][hapmap]
rs7850958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854570	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7872648	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7874310	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7874388	0.90[JPT][hapmap]
rs879492	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881791	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs963774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3737142	SYK	cis	parietal	SCAN
rs3737142	LOC57653	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
2	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
4	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
5	chr9:97920400-97951800	Weak transcription	HepG2	liver
6	chr9:97920600-97933400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:97925800-97938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:97925800-97944800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:97926000-97937800	Weak transcription	Psoas Muscle	Psoas
10	chr9:97926400-97934400	Weak transcription	Primary B cells from cord blood	blood
11	chr9:97927600-97950400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:97930000-97945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:97930000-97945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:97930600-97939400	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:97930600-97943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:97930600-97944800	Weak transcription	Lung	lung
17	chr9:97930600-97950400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:97930600-97950800	Weak transcription	Thymus	Thymus
19	chr9:97930600-97952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:97930800-97933600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:97930800-97940400	Weak transcription	Fetal Thymus	thymus
22	chr9:97930800-97941600	Weak transcription	Liver	Liver
23	chr9:97930800-97951600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:97931000-97933800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:97931200-97937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:97931200-97940000	Weak transcription	Fetal Intestine Small	intestine
28	chr9:97931800-97937800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:97932000-97934000	Enhancers	Fetal Heart	heart
30	chr9:97932000-97935000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr9:97932200-97933800	Weak transcription	Dnd41	blood
32	chr9:97932200-97944800	Weak transcription	Primary T cells from cord blood	blood
33	chr9:97932200-97945000	Weak transcription	Fetal Intestine Large	intestine
34	chr9:97932600-97933800	Enhancers	Fetal Lung	lung
35	chr9:97932600-97934200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:97932800-97933400	Enhancers	Stomach Smooth Muscle	stomach
37	chr9:97932800-97933600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:97932800-97933800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:97932800-97934000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97932800-97934200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr9:97932800-97934200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:97932800-97934200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr9:97932800-97934200	Enhancers	GM12878-XiMat	blood
44	chr9:97933000-97933400	Enhancers	Fetal Kidney	kidney
45	chr9:97933000-97933400	Flanking Active TSS	HUVEC	blood vessel
46	chr9:97933000-97933600	Enhancers	Adipose Nuclei	Adipose
47	chr9:97933000-97933600	Enhancers	Fetal Stomach	stomach
48	chr9:97933000-97933600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:97933000-97933600	Enhancers	A549	lung
50	chr9:97933000-97933600	Enhancers	Hela-S3	cervix

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