Variant report

Variant	rs7028939
Chromosome Location	chr9:102808685-102808686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102807697..102809617-chr9:102824304..102827110,2	K562	blood:
2	chr9:102806476..102810121-chr9:102811764..102815000,3	K562	blood:
3	chr9:102806680..102809036-chr9:102815147..102817165,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10117638	0.86[YRI][hapmap]
rs10512269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs1055187	0.83[ASW][hapmap];0.90[YRI][hapmap]
rs10739792	0.86[YRI][hapmap]
rs10760707	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760708	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760719	1.00[CEU][hapmap]
rs10760722	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap]
rs10819718	0.94[EUR][1000 genomes]
rs10819721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs10819726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs10819727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs10819730	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10819731	1.00[CEU][hapmap]
rs10819732	1.00[CEU][hapmap]
rs10819747	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs10819748	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs10988932	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988936	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988944	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988948	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988952	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988954	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10988955	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988956	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988957	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988960	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988964	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988966	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988972	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10988978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[MKK][hapmap];0.80[EUR][1000 genomes]
rs10988979	0.80[EUR][1000 genomes]
rs10988982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap]
rs10988984	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988988	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs10988993	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988994	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10988996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs10989003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs10989004	1.00[CEU][hapmap]
rs10989007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs10989010	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989013	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989017	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989018	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs10989019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs10989020	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11515448	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789482	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11794753	0.89[CEU][hapmap]
rs11998890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12003061	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs12003124	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs12377746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs1338120	1.00[CHB][hapmap]
rs1415927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs14297	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1529195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919002	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs16919015	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2416986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap]
rs57875316	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs6479006	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7020150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020780	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap]
rs7021923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7022208	0.86[YRI][hapmap]
rs7022643	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7025271	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7025412	1.00[CEU][hapmap]
rs7026341	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026529	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026567	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7028564	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7031081	0.85[EUR][1000 genomes]
rs7033350	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap]
rs7041818	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7043946	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7047693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7350268	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73505717	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73505783	0.80[EUR][1000 genomes]
rs7849323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850961	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7853497	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7853561	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7853585	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7853672	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7854689	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7856932	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7857556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7858045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7860268	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7860660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7862614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7865483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7866669	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7866950	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7867803	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap]
rs7868446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs7870469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7872897	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap]
rs7873545	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Preeclampsia	23551011	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7028939	CYLC2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102729600-102826800	Weak transcription	HMEC	breast
2	chr9:102767000-102820400	Weak transcription	Colonic Mucosa	Colon
3	chr9:102767200-102821800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:102767600-102826400	Weak transcription	Small Intestine	intestine
5	chr9:102767600-102845600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:102767800-102830000	Weak transcription	HSMMtube	muscle
7	chr9:102767800-102835600	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:102771400-102816200	Weak transcription	NH-A	brain
9	chr9:102778400-102813200	Weak transcription	HUVEC	blood vessel
10	chr9:102781800-102811000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:102782000-102813000	Weak transcription	HSMM	muscle
12	chr9:102782600-102812400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:102782600-102813200	Weak transcription	Placenta	Placenta
14	chr9:102783800-102814000	Weak transcription	Osteobl	bone
15	chr9:102783800-102819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:102784000-102813200	Weak transcription	NHEK	skin
17	chr9:102788600-102825600	Weak transcription	A549	lung
18	chr9:102790800-102808800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:102790800-102809200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:102791000-102810800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:102791000-102813000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:102792800-102812800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:102793400-102813000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:102795200-102810800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:102796400-102811000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr9:102796400-102813000	Weak transcription	Fetal Thymus	thymus
27	chr9:102796400-102826000	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:102796400-102828800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:102796800-102812800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:102796800-102813400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:102797200-102808800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:102797200-102812800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr9:102797200-102815400	Weak transcription	HepG2	liver
34	chr9:102797400-102821000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:102797400-102827800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:102798600-102813400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:102799000-102812400	Weak transcription	Dnd41	blood
38	chr9:102799200-102810800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:102799800-102811800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:102799800-102813000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:102800000-102809200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:102800000-102810800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:102800000-102811400	Weak transcription	Liver	Liver
44	chr9:102800000-102813000	Weak transcription	Left Ventricle	heart
45	chr9:102800000-102817600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:102800000-102819200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:102800000-102820400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:102800000-102828800	Weak transcription	Aorta	Aorta
49	chr9:102800000-102828800	Weak transcription	Gastric	stomach
50	chr9:102800000-102828800	Weak transcription	Pancreas	Pancrea

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