Variant report

Variant	rs11963138
Chromosome Location	chr6:2264559-2264560
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2263398..2266340-chr6:2266756..2269445,2	K562	blood:
2	chr6:2243938..2247142-chr6:2264459..2268782,4	MCF-7	breast:
3	chr6:2259328..2261334-chr6:2262828..2265000,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112699	Chromatin interaction
ENSG00000250903	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11242758	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11961324	0.94[ASN][1000 genomes]
rs11962550	0.82[ASN][1000 genomes]
rs11963529	0.97[ASN][1000 genomes]
rs12191002	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12661136	0.97[ASN][1000 genomes]
rs13196306	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13217030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295008	0.98[ASN][1000 genomes]
rs2450299	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450304	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450307	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450310	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479001	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479002	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479004	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479008	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479011	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2479014	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2505657	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505658	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505659	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505660	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505661	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505662	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505663	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505666	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505667	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505670	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505671	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505673	0.85[ASN][1000 genomes]
rs2505677	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505678	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36016883	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3778568	0.97[ASN][1000 genomes]
rs3800184	0.94[ASN][1000 genomes]
rs3800185	0.94[ASN][1000 genomes]
rs3800187	0.97[ASN][1000 genomes]
rs3800190	0.97[ASN][1000 genomes]
rs3823287	1.00[ASN][1000 genomes]
rs55992523	0.96[ASN][1000 genomes]
rs56196406	0.97[ASN][1000 genomes]
rs6596879	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72830182	0.94[ASN][1000 genomes]
rs72830184	0.97[ASN][1000 genomes]
rs7754950	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328087	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378686	0.94[ASN][1000 genomes]
rs9378687	0.94[ASN][1000 genomes]
rs9378688	1.00[ASN][1000 genomes]
rs9378692	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378693	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391946	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392373	0.92[ASN][1000 genomes]
rs9392374	0.97[ASN][1000 genomes]
rs9392375	1.00[ASN][1000 genomes]
rs9392377	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405550	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11963138	LOC728772///TMEM106A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2247000-2264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:2247000-2265200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:2247000-2265200	Weak transcription	Osteobl	bone
4	chr6:2247000-2269400	Weak transcription	Right Ventricle	heart
5	chr6:2247000-2273800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:2247000-2275000	Weak transcription	Fetal Kidney	kidney
7	chr6:2247000-2275400	Weak transcription	NHLF	lung
8	chr6:2247000-2275600	Weak transcription	Fetal Heart	heart
9	chr6:2247200-2272600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:2247600-2274400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:2247800-2284200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:2248200-2275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:2248400-2274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:2250400-2267600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:2250400-2274800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:2250800-2265400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:2251000-2273600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:2252200-2264800	Weak transcription	Fetal Thymus	thymus
19	chr6:2252400-2265800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:2255200-2272400	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:2255400-2265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:2255400-2272800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:2255600-2269600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:2255800-2288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:2256000-2269400	Weak transcription	Fetal Lung	lung
26	chr6:2256000-2272400	Weak transcription	Placenta	Placenta
27	chr6:2256200-2272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:2256200-2272600	Weak transcription	Brain Substantia Nigra	brain
29	chr6:2256200-2272800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:2258800-2265800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:2258800-2271000	Weak transcription	Colonic Mucosa	Colon
32	chr6:2259800-2265200	Weak transcription	NHDF-Ad	bronchial
33	chr6:2259800-2276400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:2261600-2272000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:2261800-2272800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:2262200-2267000	Weak transcription	Stomach Mucosa	stomach
37	chr6:2262200-2282600	Weak transcription	Small Intestine	intestine
38	chr6:2263600-2264600	ZNF genes & repeats	HepG2	liver
39	chr6:2263800-2265600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr6:2264000-2264600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr6:2264000-2279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:2264200-2264600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:2264200-2264600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:2264200-2264600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:2264200-2264600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:2264200-2264600	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr6:2264200-2264600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
48	chr6:2264200-2264600	ZNF genes & repeats	Lung	lung
49	chr6:2264200-2264600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
50	chr6:2264200-2264600	ZNF genes & repeats	HSMM	muscle

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