Variant report

Variant	rs7558931
Chromosome Location	chr2:98438834-98438835
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10176201	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10182941	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs10194485	1.00[YRI][hapmap]
rs10200949	0.81[EUR][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs11123869	0.83[MEX][hapmap];0.94[MKK][hapmap]
rs11123924	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11123949	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11899171	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712123	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712174	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs13010946	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13034644	0.83[AMR][1000 genomes]
rs1317178	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13405546	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1466020	0.94[CEU][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1466924	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1922282	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2091772	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2100058	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2141862	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2279826	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2309316	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309317	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3762593	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4274643	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4560167	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5865	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs6543108	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6543109	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6543161	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6543177	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6543202	0.83[EUR][1000 genomes]
rs6543210	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs6707924	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6709571	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs6710813	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6712517	0.84[CEU][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs6719556	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6723466	0.83[AMR][1000 genomes]
rs6723653	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6744331	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6748809	0.86[CHB][hapmap]
rs6748927	0.83[CHB][hapmap]
rs7561104	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7562695	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7567397	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7574437	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7582664	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7586210	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs930607	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9308862	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9973416	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv961841	chr2:98437476-98446329	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7558931	FAM178B	cis	parietal	SCAN
rs7558931	ANKRD39	cis	cerebellum	SCAN
rs7558931	ANKRD36B	cis	Nerve Tibial	GTEx
rs7558931	ADRA2B	cis	cerebellum	SCAN
rs7558931	CNNM3	cis	cerebellum	SCAN
rs7558931	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs7558931	ANKRD36B	cis	Artery Aorta	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
3	chr2:98406400-98469200	Weak transcription	A549	lung
4	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
5	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
6	chr2:98410000-98446000	Weak transcription	Colonic Mucosa	Colon
7	chr2:98410000-98456200	Weak transcription	Thymus	Thymus
8	chr2:98410000-98456800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:98410000-98456800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:98410000-98457400	Weak transcription	Small Intestine	intestine
11	chr2:98422000-98456200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:98424000-98442600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:98424000-98446800	Weak transcription	Fetal Heart	heart
14	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:98425600-98456800	Weak transcription	Esophagus	oesophagus
17	chr2:98425600-98461000	Weak transcription	Brain Germinal Matrix	brain
18	chr2:98426000-98445400	Weak transcription	Gastric	stomach
19	chr2:98426000-98456800	Weak transcription	Right Ventricle	heart
20	chr2:98426200-98456800	Weak transcription	Pancreas	Pancrea
21	chr2:98426400-98456200	Weak transcription	NHEK	skin
22	chr2:98426400-98456800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:98428000-98466600	Weak transcription	K562	blood
24	chr2:98428200-98456600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:98428400-98447400	Weak transcription	Psoas Muscle	Psoas
26	chr2:98428600-98447400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:98428600-98448800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:98428600-98456000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:98428600-98456600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:98428600-98461200	Weak transcription	Fetal Brain Male	brain
31	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
32	chr2:98428800-98485000	Weak transcription	NHLF	lung
33	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:98429200-98448600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:98429200-98448800	Weak transcription	Fetal Kidney	kidney
36	chr2:98429200-98456600	Weak transcription	Fetal Lung	lung
37	chr2:98429800-98439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:98430200-98445200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:98430600-98456200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:98430600-98456800	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:98430800-98439000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:98430800-98445400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:98430800-98448800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:98430800-98448800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:98430800-98448800	Weak transcription	Brain Anterior Caudate	brain
47	chr2:98430800-98449000	Weak transcription	HMEC	breast
48	chr2:98430800-98456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:98430800-98456000	Weak transcription	Ovary	ovary
50	chr2:98431000-98448600	Weak transcription	Muscle Satellite Cultured Cells	--

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