Variant report

Variant	rs9392377
Chromosome Location	chr6:2275206-2275207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11242758	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11961324	0.94[ASN][1000 genomes]
rs11962550	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11963138	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963529	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12191002	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12661136	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13196306	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13217030	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295008	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2450299	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450304	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450307	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479001	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479002	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479004	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479008	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479011	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2479014	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505657	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505658	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505659	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505660	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505661	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505662	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505663	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505666	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505667	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505670	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505671	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505673	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505677	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505678	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36016883	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3778568	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3800184	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3800185	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800187	0.97[ASN][1000 genomes]
rs3800190	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs3823287	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs55992523	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs56196406	0.97[ASN][1000 genomes]
rs6596879	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72830182	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72830184	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7754950	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328087	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378686	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs9378687	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs9378688	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs9378692	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378693	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391946	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392373	0.92[ASN][1000 genomes]
rs9392374	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs9392375	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs9405550	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
9	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
12	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
15	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
16	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9392377	LOC728772///TMEM106A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2247000-2275400	Weak transcription	NHLF	lung
2	chr6:2247000-2275600	Weak transcription	Fetal Heart	heart
3	chr6:2247800-2284200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:2255800-2288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:2259800-2276400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:2262200-2282600	Weak transcription	Small Intestine	intestine
7	chr6:2264000-2279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:2264400-2285800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:2264600-2286400	Weak transcription	HSMM	muscle
10	chr6:2265600-2278200	Weak transcription	Psoas Muscle	Psoas
11	chr6:2265800-2276000	Weak transcription	HSMMtube	muscle
12	chr6:2266800-2276400	Weak transcription	Fetal Brain Male	brain
13	chr6:2267400-2279800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:2267600-2276200	Strong transcription	Primary T cells from cord blood	blood
15	chr6:2268200-2275600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:2268400-2275800	Weak transcription	Stomach Mucosa	stomach
17	chr6:2269000-2275600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:2269800-2275800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:2270200-2275400	Strong transcription	Fetal Intestine Large	intestine
20	chr6:2270200-2275600	Strong transcription	Fetal Intestine Small	intestine
21	chr6:2270800-2275400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:2271400-2276400	Strong transcription	HepG2	liver
23	chr6:2271400-2287600	Weak transcription	Right Ventricle	heart
24	chr6:2272200-2275600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:2272400-2275800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr6:2272600-2275400	Strong transcription	Gastric	stomach
27	chr6:2272600-2275600	Strong transcription	Left Ventricle	heart
28	chr6:2273000-2288200	Weak transcription	Aorta	Aorta
29	chr6:2273200-2276400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:2273200-2278800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:2273400-2276400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:2273400-2276400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:2273400-2278200	Weak transcription	GM12878-XiMat	blood
34	chr6:2273400-2282000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:2273600-2275800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:2273600-2281200	Weak transcription	Placenta	Placenta
37	chr6:2273600-2284400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:2273600-2286000	Weak transcription	Fetal Thymus	thymus
39	chr6:2273600-2286600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:2273600-2286600	Weak transcription	Pancreas	Pancrea
41	chr6:2273600-2286800	Weak transcription	Colonic Mucosa	Colon
42	chr6:2273600-2288200	Weak transcription	Spleen	Spleen
43	chr6:2273800-2276000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:2273800-2276600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:2273800-2278200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:2273800-2284000	Weak transcription	Thymus	Thymus
47	chr6:2273800-2288800	Weak transcription	Brain Anterior Caudate	brain
48	chr6:2274000-2283800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:2274200-2275600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr6:2274200-2286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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