Variant report

Variant	rs2290124
Chromosome Location	chr2:98273661-98273662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1020396	0.81[CHB][hapmap]
rs1042705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496323	0.81[CHB][hapmap]
rs11123849	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680855	0.81[CHB][hapmap]
rs11893601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11894651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12991969	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001139	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001728	0.81[CEU][hapmap]
rs13003963	0.91[ASN][1000 genomes]
rs13009163	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034349	0.81[CHB][hapmap]
rs1375436	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463174	0.81[CHB][hapmap]
rs1470625	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2053824	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167007	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276644	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276645	0.81[CHB][hapmap]
rs3474	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542980	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873886	0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	esv2756939	chr2:97708611-98274527	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv2763630	chr2:97731133-98279050	Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv431413	chr2:97753585-98274527	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1001249	chr2:97972600-98274527	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv999627	chr2:98013814-98274527	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	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
13	nsv582512	chr2:98272634-98277804	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2290124	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs2290124	ANKRD36B	cis	Nerve Tibial	GTEx
rs2290124	CNNM3	cis	cerebellum	SCAN
rs2290124	ZAP70	cis	Nerve Tibial	GTEx
rs2290124	ANKRD36B	cis	Artery Tibial	GTEx
rs2290124	ANKRD36B	cis	Thyroid	GTEx
rs2290124	ANKRD39	cis	cerebellum	SCAN
rs2290124	INPP4A	cis	cerebellum	SCAN
rs2290124	ACTR1B	cis	cerebellum	SCAN
rs2290124	ANKRD36B	cis	lung	GTEx
rs2290124	ANKRD36B	cis	cerebellum	SCAN
rs2290124	ZAP70	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98264600-98277400	Weak transcription	Right Atrium	heart
2	chr2:98265200-98276800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:98265200-98277200	Weak transcription	HUVEC	blood vessel
4	chr2:98265600-98274400	Weak transcription	Psoas Muscle	Psoas
5	chr2:98265600-98277600	Weak transcription	Small Intestine	intestine
6	chr2:98265600-98277800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:98265800-98277200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:98266600-98277200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:98269000-98275200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:98270000-98275600	Strong transcription	Primary B cells from cord blood	blood
11	chr2:98270000-98275600	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr2:98270200-98275800	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr2:98270200-98276800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:98270200-98277200	Strong transcription	Brain Cingulate Gyrus	brain
15	chr2:98270400-98275400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:98270400-98277200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:98270400-98278200	Strong transcription	Primary T cells from cord blood	blood
18	chr2:98270400-98278200	Weak transcription	Stomach Mucosa	stomach
19	chr2:98270600-98277000	Strong transcription	Osteobl	bone
20	chr2:98270600-98277400	Strong transcription	Dnd41	blood
21	chr2:98270600-98277600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:98270600-98277800	Strong transcription	Thymus	Thymus
23	chr2:98270800-98276000	Strong transcription	Pancreas	Pancrea
24	chr2:98270800-98276400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:98270800-98276400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:98270800-98276800	Strong transcription	Right Ventricle	heart
27	chr2:98270800-98277400	Strong transcription	Rectal Smooth Muscle	rectum
28	chr2:98271000-98275400	Strong transcription	NHDF-Ad	bronchial
29	chr2:98271000-98275800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:98271000-98276800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:98271000-98277200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:98271000-98278000	Weak transcription	Fetal Brain Male	brain
33	chr2:98271200-98275200	Weak transcription	Fetal Heart	heart
34	chr2:98271200-98275800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:98271200-98276000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:98271200-98276000	Strong transcription	Ovary	ovary
37	chr2:98271200-98277000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:98271200-98277200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:98271200-98277200	Strong transcription	Adipose Nuclei	Adipose
40	chr2:98271200-98277600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:98271200-98277800	Strong transcription	Colonic Mucosa	Colon
42	chr2:98271200-98278000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:98271400-98274600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:98271400-98276000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:98271400-98276800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:98271400-98276800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:98271400-98277000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:98271400-98277400	Strong transcription	Liver	Liver
49	chr2:98271400-98278000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:98271400-98278600	Weak transcription	Fetal Kidney	kidney

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