Variant report

Variant	rs11249930
Chromosome Location	chr8:9472445-9472446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:9472444-9472917	SK-N-MC	brain:	n/a	n/a
2	KAP1	chr8:9471230-9473125	U2OS	brain:	n/a	n/a
3	SPI1	chr8:9472252-9472916	HL-60	blood:	n/a	n/a
4	SPI1	chr8:9472393-9472688	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:9472328-9472983	HL-60	blood:	n/a	n/a
6	KAP1	chr8:9471738-9473064	HEK293	kidney:	n/a	n/a
7	EBF1	chr8:9472410-9472729	GM12878	blood:	n/a	n/a
8	SPI1	chr8:9472418-9472686	GM12891	blood:	n/a	n/a
9	RUNX3	chr8:9472376-9472835	GM12878	blood:	n/a	n/a
10	RUNX3	chr8:9472422-9472850	GM12878	blood:	n/a	n/a
11	GATA3	chr8:9472246-9472494	SH-SY5Y	brain:	n/a	n/a
12	MYC	chr8:9472436-9472837	NB4	blood:	n/a	n/a
13	POLR2A	chr8:9472367-9472919	SK-N-MC	brain:	n/a	n/a
14	NFIC	chr8:9472223-9472882	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
TNKS	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10094343	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10104247	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249943	0.93[MEX][hapmap];0.81[TSI][hapmap]
rs11784181	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12335065	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542420	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12544673	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12549064	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs28437757	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28464158	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28610188	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28615758	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240630	0.82[EUR][1000 genomes]
rs4265191	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4416825	0.85[ASN][1000 genomes]
rs4427176	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4457339	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4481595	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4560795	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4562329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4573280	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4841178	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4841180	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4841184	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4841200	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap]
rs62491543	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62491544	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62493907	0.86[ASN][1000 genomes]
rs62493909	0.84[ASN][1000 genomes]
rs62493910	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62493913	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6601341	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6982215	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6996829	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7006406	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7464476	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7814014	0.81[MEX][hapmap]
rs7821799	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7825818	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs7827278	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7829326	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7833036	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11249930	TNKS	cis	parietal	SCAN
rs11249930	MFHAS1	cis	cerebellum	SCAN
rs11249930	PRSS55	cis	cerebellum	SCAN
rs11249930	DEFB136	cis	cerebellum	SCAN
rs11249930	BLK	cis	parietal	SCAN
rs11249930	DEFB134	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9435800-9472600	Weak transcription	HSMMtube	muscle
2	chr8:9450600-9480200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr8:9461000-9486400	Weak transcription	Fetal Intestine Small	intestine
4	chr8:9462200-9473800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:9463000-9479800	Weak transcription	Dnd41	blood
6	chr8:9463200-9480600	Weak transcription	Primary T cells from cord blood	blood
7	chr8:9466200-9473000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:9466200-9480000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr8:9466200-9484400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr8:9466400-9472600	Weak transcription	Primary B cells from cord blood	blood
11	chr8:9466400-9472600	Weak transcription	Pancreas	Pancrea
12	chr8:9466400-9472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:9466400-9479800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr8:9466400-9483200	Weak transcription	Liver	Liver
15	chr8:9466400-9484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:9466400-9485400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr8:9466400-9491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:9467000-9472600	Weak transcription	Right Ventricle	heart
19	chr8:9468400-9472800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr8:9468800-9472600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:9468800-9472800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr8:9468800-9473800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr8:9468800-9474600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:9468800-9476600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr8:9469000-9473800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr8:9469000-9476600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr8:9470200-9473800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr8:9470400-9472600	Enhancers	Stomach Mucosa	stomach
29	chr8:9470400-9474600	Enhancers	Fetal Heart	heart
30	chr8:9470400-9475000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:9470600-9472600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr8:9470600-9472600	Weak transcription	Right Atrium	heart
33	chr8:9470600-9473000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:9470600-9473000	Enhancers	Brain Substantia Nigra	brain
35	chr8:9470600-9473200	Enhancers	Brain Angular Gyrus	brain
36	chr8:9470600-9473200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr8:9470600-9473800	Enhancers	Colon Smooth Muscle	Colon
38	chr8:9470600-9474600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr8:9470800-9472600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr8:9470800-9472600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr8:9470800-9472800	Weak transcription	Left Ventricle	heart
42	chr8:9470800-9473200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr8:9470800-9476200	Weak transcription	Placenta	Placenta
44	chr8:9470800-9476800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:9471000-9472600	Weak transcription	Psoas Muscle	Psoas
46	chr8:9471000-9472800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:9471000-9473200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr8:9471000-9479800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr8:9471000-9487000	Weak transcription	HepG2	liver
50	chr8:9471200-9472600	Enhancers	Rectal Smooth Muscle	rectum

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