Variant report

Variant	rs6725184
Chromosome Location	chr2:32330885-32330886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10208246	0.91[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap]
rs10439444	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs10490360	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs11124274	0.83[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11124275	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs11124276	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11124277	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11676938	0.94[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11678119	0.94[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap]
rs11681731	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11683760	0.85[AFR][1000 genomes]
rs11683931	0.85[AFR][1000 genomes]
rs11686061	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11691939	0.83[CHB][hapmap]
rs11694630	0.85[AFR][1000 genomes]
rs12465351	0.87[CHB][hapmap]
rs12474443	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12611678	0.85[AFR][1000 genomes]
rs12614686	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs12617289	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12617290	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12618002	0.85[AFR][1000 genomes]
rs12989936	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap]
rs12995952	0.85[AFR][1000 genomes]
rs12997026	0.87[CHB][hapmap]
rs13007972	0.83[AFR][1000 genomes]
rs13017189	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap]
rs13022197	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13427170	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs13431540	0.81[ASN][1000 genomes]
rs160797	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs17011801	0.83[CHB][hapmap]
rs17767988	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[YRI][hapmap]
rs212679	0.95[CEU][hapmap]
rs212699	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[YRI][hapmap]
rs212701	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[YRI][hapmap]
rs212703	0.86[CHD][hapmap]
rs212714	0.91[GIH][hapmap]
rs212715	0.94[CEU][hapmap]
rs212716	0.82[ASW][hapmap];0.89[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap]
rs212717	0.82[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap]
rs212721	0.82[YRI][hapmap]
rs212724	0.94[CEU][hapmap];0.86[YRI][hapmap]
rs212726	0.94[CEU][hapmap]
rs212727	0.94[CEU][hapmap];0.89[GIH][hapmap]
rs212730	0.94[CEU][hapmap];0.80[LWK][hapmap];0.82[YRI][hapmap]
rs212731	0.94[CEU][hapmap];0.84[GIH][hapmap]
rs212737	0.89[CEU][hapmap];0.82[GIH][hapmap];0.81[LWK][hapmap];0.87[YRI][hapmap]
rs212738	0.87[CHB][hapmap]
rs212739	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs212745	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs212746	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs212755	0.80[LWK][hapmap]
rs212758	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs212759	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs212760	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs216544	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2235134	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2280967	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap]
rs2294176	0.84[AFR][1000 genomes]
rs2294179	0.81[AFR][1000 genomes]
rs2365555	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.96[MEX][hapmap]
rs2365558	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2366736	0.87[CHB][hapmap]
rs36014814	0.86[AFR][1000 genomes]
rs3752916	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3769602	0.84[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap]
rs3769604	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769605	0.83[CHB][hapmap]
rs3769606	0.94[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs385076	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap]
rs3851310	0.89[CEU][hapmap]
rs430759	0.94[CEU][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap]
rs435572	0.82[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap]
rs443609	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap]
rs455060	0.94[CEU][hapmap];0.81[LWK][hapmap]
rs467523	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs469305	0.85[CEU][hapmap]
rs479333	0.82[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap]
rs4952209	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs4952247	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4952248	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap]
rs4952249	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4952250	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4952252	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap]
rs6543649	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs659239	0.82[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap]
rs6716179	0.83[LWK][hapmap]
rs6717209	0.87[CHB][hapmap]
rs6723154	0.82[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs6737500	0.83[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap]
rs6738349	0.82[EUR][1000 genomes]
rs6747488	0.84[EUR][1000 genomes]
rs6748621	0.89[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs6752375	0.83[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6758024	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[YRI][hapmap]
rs6760105	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs7559964	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7561519	0.94[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.84[EUR][1000 genomes]
rs7566162	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7572964	0.84[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7573543	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7577408	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7577696	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap]
rs7581032	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7581340	0.94[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7581432	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs7586448	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs7588883	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap]
rs7592239	0.82[AFR][1000 genomes]
rs7592356	0.83[AFR][1000 genomes]
rs7601267	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs7604289	0.83[AFR][1000 genomes]
rs7605242	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9677104	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9750659	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9752631	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv873779	chr2:32330885-32372245	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6725184	EHD3	cis	parietal	SCAN
rs6725184	DPY30	cis	parietal	SCAN
rs6725184	NLRC4	cis	lymphoblastoid	seeQTL
rs6725184	NLRC4	cis	Lymphoblastoid	GTEx
rs6725184	SLC30A6	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32290400-32331000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:32290400-32353400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:32291000-32332600	Weak transcription	A549	lung
4	chr2:32291400-32331000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:32291600-32332200	Weak transcription	HUVEC	blood vessel
6	chr2:32292000-32343200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:32292600-32353800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:32295800-32353800	Weak transcription	Fetal Brain Male	brain
9	chr2:32296400-32362600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:32297600-32360600	Weak transcription	Osteobl	bone
11	chr2:32298800-32341400	Weak transcription	Small Intestine	intestine
12	chr2:32300000-32339600	Weak transcription	HepG2	liver
13	chr2:32309800-32381200	Weak transcription	NHDF-Ad	bronchial
14	chr2:32311800-32331000	Weak transcription	Gastric	stomach
15	chr2:32312600-32331000	Weak transcription	Colonic Mucosa	Colon
16	chr2:32313200-32360600	Weak transcription	NH-A	brain
17	chr2:32315400-32331000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:32316000-32353600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:32316200-32331200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:32316200-32343200	Weak transcription	HSMM	muscle
21	chr2:32317600-32331000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:32319800-32331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:32322200-32353400	Weak transcription	K562	blood
24	chr2:32325400-32353800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:32326000-32352200	Weak transcription	HSMMtube	muscle
26	chr2:32329400-32331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:32329600-32331000	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:32329600-32333000	Strong transcription	Primary T cells from cord blood	blood
29	chr2:32330200-32331000	Strong transcription	Fetal Intestine Large	intestine
30	chr2:32330200-32331000	ZNF genes & repeats	Fetal Lung	lung
31	chr2:32330200-32331600	ZNF genes & repeats	Ovary	ovary
32	chr2:32330200-32332000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:32330200-32332200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
34	chr2:32330200-32332400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr2:32330200-32332600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:32330200-32333000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:32330200-32333000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:32330200-32333000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:32330200-32333200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr2:32330200-32333200	Strong transcription	Liver	Liver
41	chr2:32330200-32333400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:32330200-32333600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:32330200-32333600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:32330200-32334000	Strong transcription	Fetal Thymus	thymus
45	chr2:32330400-32331000	Strong transcription	Brain Hippocampus Middle	brain
46	chr2:32330400-32331200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr2:32330400-32331600	Strong transcription	Brain Anterior Caudate	brain
48	chr2:32330400-32332200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:32330400-32332200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr2:32330400-32332400	Strong transcription	Primary T cells fromperipheralblood	blood

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