Variant report

Variant	rs7598116
Chromosome Location	chr2:98575891-98575892
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10176201	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10200949	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10211231	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1071885	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865055	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123924	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11123949	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11123966	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690482	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693874	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11888323	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899171	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12712123	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13003978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006817	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008503	0.83[ASN][1000 genomes]
rs13010946	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13022778	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034644	0.83[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[ASN][1000 genomes]
rs13405546	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1466924	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1503200	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922280	0.90[ASN][1000 genomes]
rs1922282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2091772	0.82[ASN][1000 genomes]
rs2100058	0.84[ASN][1000 genomes]
rs2141862	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279825	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2309316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs2309317	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2309356	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088327	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762593	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4560167	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs5865	0.81[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6543109	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543161	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543177	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6543202	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707924	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6709571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710813	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6719556	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6723466	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6723653	0.92[ASN][1000 genomes]
rs6744331	0.89[ASN][1000 genomes]
rs6748809	0.84[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[TSI][hapmap]
rs7561104	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7562695	0.88[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7574437	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577886	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582664	0.88[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602412	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605180	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930607	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9308862	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs956696	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9973416	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7598116	CNNM3	cis	cerebellum	SCAN
rs7598116	ADRA2B	cis	cerebellum	SCAN
rs7598116	ZAP70	cis	cerebellum	SCAN
rs7598116	ZAP70	cis	Nerve Tibial	GTEx
rs7598116	FAM178B	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:98567600-98586600	Weak transcription	Fetal Stomach	stomach
4	chr2:98568000-98578200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:98568000-98583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:98568200-98580800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98568400-98586600	Weak transcription	Aorta	Aorta
9	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:98569200-98579400	Weak transcription	Esophagus	oesophagus
11	chr2:98569200-98579600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:98569200-98580600	Weak transcription	NHDF-Ad	bronchial
13	chr2:98569200-98581400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:98571000-98579400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:98571000-98586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:98574000-98578400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:98574200-98576000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:98574200-98577800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:98574200-98580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:98574400-98576000	Enhancers	Psoas Muscle	Psoas
21	chr2:98574400-98586200	Weak transcription	NH-A	brain
22	chr2:98574600-98582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:98574600-98583200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:98574600-98583400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:98574800-98579200	Weak transcription	Fetal Heart	heart
26	chr2:98574800-98585200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:98574800-98586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:98575000-98578000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:98575000-98583000	Weak transcription	Gastric	stomach
30	chr2:98575000-98585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:98575000-98586800	Weak transcription	Brain Angular Gyrus	brain
32	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:98575200-98576800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:98575200-98576800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:98575200-98576800	Weak transcription	HMEC	breast
36	chr2:98575200-98578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:98575200-98579000	Weak transcription	NHEK	skin
38	chr2:98575200-98579200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:98575200-98579600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:98575200-98580600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:98575200-98580600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:98575200-98583000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:98575200-98583200	Weak transcription	Small Intestine	intestine
44	chr2:98575200-98584400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:98575400-98577000	Weak transcription	GM12878-XiMat	blood
47	chr2:98575400-98579200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:98575400-98579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:98575400-98579400	Weak transcription	Primary T cells from cord blood	blood
50	chr2:98575400-98581400	Weak transcription	Left Ventricle	heart

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