Variant report

Variant	rs9942602
Chromosome Location	chr7:17977054-17977055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:17966773..17969755-chr7:17976526..17979737,3	K562	blood:
2	chr7:17936656..17938399-chr7:17976811..17978659,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10216315	0.84[ASN][1000 genomes]
rs10227224	0.87[ASN][1000 genomes]
rs10227501	0.83[ASN][1000 genomes]
rs10227582	0.87[ASN][1000 genomes]
rs10231926	0.84[ASN][1000 genomes]
rs10265373	0.83[ASN][1000 genomes]
rs11768866	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11983260	0.83[ASN][1000 genomes]
rs12699918	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357796	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1404414	0.80[EUR][1000 genomes]
rs1404424	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1524774	0.80[EUR][1000 genomes]
rs1524775	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1568815	0.84[ASN][1000 genomes]
rs1568817	0.85[ASN][1000 genomes]
rs1568818	0.85[ASN][1000 genomes]
rs2103144	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2140710	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2177652	0.86[ASN][1000 genomes]
rs2691552	0.84[EUR][1000 genomes]
rs2691555	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691557	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691558	0.85[ASN][1000 genomes]
rs2691559	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691560	0.84[ASN][1000 genomes]
rs2691561	0.84[ASN][1000 genomes]
rs2691562	0.84[ASN][1000 genomes]
rs2691563	0.84[ASN][1000 genomes]
rs2691564	0.84[ASN][1000 genomes]
rs2691566	0.84[ASN][1000 genomes]
rs2691567	0.82[ASN][1000 genomes]
rs2691568	0.84[ASN][1000 genomes]
rs2691569	0.84[ASN][1000 genomes]
rs2691570	0.84[ASN][1000 genomes]
rs2691571	0.84[ASN][1000 genomes]
rs2691580	0.80[ASN][1000 genomes]
rs2691597	0.80[EUR][1000 genomes]
rs2691600	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2691601	0.82[EUR][1000 genomes]
rs2691602	0.81[EUR][1000 genomes]
rs2691605	0.82[EUR][1000 genomes]
rs2691607	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2691609	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691611	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2691612	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691613	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691615	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691618	0.83[EUR][1000 genomes]
rs2691620	0.83[EUR][1000 genomes]
rs2691623	0.80[ASN][1000 genomes]
rs2714857	0.83[ASN][1000 genomes]
rs2714859	0.85[ASN][1000 genomes]
rs2714860	0.84[ASN][1000 genomes]
rs2714861	0.84[ASN][1000 genomes]
rs2714863	0.83[ASN][1000 genomes]
rs2714864	0.84[ASN][1000 genomes]
rs2714865	0.84[ASN][1000 genomes]
rs2714866	0.84[ASN][1000 genomes]
rs2714867	0.83[ASN][1000 genomes]
rs2714868	0.84[ASN][1000 genomes]
rs2714869	0.85[ASN][1000 genomes]
rs2714870	0.84[ASN][1000 genomes]
rs2714876	0.84[EUR][1000 genomes]
rs2714877	0.84[EUR][1000 genomes]
rs2723540	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723567	0.83[EUR][1000 genomes]
rs2723569	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723570	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2723571	0.83[EUR][1000 genomes]
rs2723572	0.83[EUR][1000 genomes]
rs35819944	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4532510	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4543433	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4719525	0.87[ASN][1000 genomes]
rs4721661	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4721665	0.82[EUR][1000 genomes]
rs4721671	0.89[ASN][1000 genomes]
rs56287412	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67452591	0.83[EUR][1000 genomes]
rs6955984	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973480	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv887808	chr7:17920613-18150005	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1018517	chr7:17926468-18127372	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv531013	chr7:17970218-18248642	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9942602	SNX13	cis	brain	BrainEAC

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:17955000-17977400	Weak transcription	Fetal Intestine Small	intestine
3	chr7:17961800-17977400	Weak transcription	Brain Angular Gyrus	brain
4	chr7:17961800-17978800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:17962200-17977400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:17962400-17978600	Weak transcription	Aorta	Aorta
7	chr7:17963400-17977400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:17963800-17977800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:17965400-17977200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:17967200-17978800	Weak transcription	Lung	lung
11	chr7:17969200-17977800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:17970600-17977400	Weak transcription	Ovary	ovary
13	chr7:17970600-17978800	Weak transcription	Pancreas	Pancrea
14	chr7:17970800-17977400	Weak transcription	Adipose Nuclei	Adipose
15	chr7:17970800-17977400	Weak transcription	Right Atrium	heart
16	chr7:17970800-17978000	Weak transcription	Left Ventricle	heart
17	chr7:17970800-17978600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:17970800-17978800	Weak transcription	Gastric	stomach
19	chr7:17971000-17977200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:17971000-17977400	Weak transcription	NHDF-Ad	bronchial
21	chr7:17971200-17977800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:17971400-17977400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:17971400-17977400	Weak transcription	Brain Substantia Nigra	brain
24	chr7:17971600-17977400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:17971800-17978200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr7:17972600-17977400	Weak transcription	Small Intestine	intestine
27	chr7:17972800-17977200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:17972800-17977200	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:17972800-17977400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:17973000-17977200	Weak transcription	Stomach Mucosa	stomach
31	chr7:17973000-17977400	Weak transcription	Right Ventricle	heart
32	chr7:17973200-17978800	Weak transcription	Spleen	Spleen
33	chr7:17973400-17977400	Weak transcription	Colonic Mucosa	Colon
34	chr7:17973600-17977200	Weak transcription	Liver	Liver
35	chr7:17973800-17977400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:17974000-17977200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:17974000-17978000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:17974200-17977400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:17974200-17978600	Weak transcription	Fetal Thymus	thymus
40	chr7:17974400-17977800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:17974600-17978000	Weak transcription	Thymus	Thymus
42	chr7:17974800-17977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:17974800-17977400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:17974800-17977600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr7:17975000-17977200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:17975000-17977200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:17975000-17977400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:17975000-17977400	Weak transcription	K562	blood
49	chr7:17975000-17978800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:17975600-17977200	Weak transcription	Monocytes-CD14+_RO01746	blood

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