Variant report

Variant	rs2112448
Chromosome Location	chr5:94038410-94038411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037940	0.81[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10039102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10039797	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10052066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10062402	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10072894	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10078522	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1031389	0.93[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10476614	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1124667	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11948061	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189060	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1451734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1549179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2112449	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2112450	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2636	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs306574	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs306578	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs306580	0.81[ASW][hapmap];0.81[GIH][hapmap]
rs421521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556849	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs747880	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs755899	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs755901	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7709494	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7735924	0.82[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][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	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2112448	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs2112448	MCTP1	cis	lymphoblastoid	seeQTL
rs2112448	C5orf36	cis	cerebellum	SCAN
rs2112448	ANKRD32	cis	parietal	SCAN
rs2112448	MCTP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
4	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
5	chr5:93996600-94048400	Weak transcription	Lung	lung
6	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
8	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
10	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
13	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:94023200-94045600	Weak transcription	Primary B cells from cord blood	blood
15	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
19	chr5:94023400-94044200	Weak transcription	Primary T cells from cord blood	blood
20	chr5:94023400-94045000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
23	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:94025800-94046200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:94025800-94050800	Weak transcription	K562	blood
28	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:94028000-94038600	Weak transcription	Fetal Lung	lung
31	chr5:94028000-94043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:94028800-94040200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:94029200-94045800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:94029200-94049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
40	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:94029400-94040400	Weak transcription	A549	lung
42	chr5:94029400-94048800	Weak transcription	HMEC	breast
43	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
44	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
45	chr5:94029800-94040800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:94029800-94050000	Weak transcription	Osteobl	bone
47	chr5:94030200-94051400	Weak transcription	HSMM	muscle
48	chr5:94031000-94038600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:94031000-94045600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:94031000-94047400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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