Variant report

Variant	rs11967455
Chromosome Location	chr6:25440445-25440446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCGN-2	chr6:25439997-25440485	NONHSAT108160

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11966296	0.81[AFR][1000 genomes]
rs73393809	1.00[AMR][1000 genomes]
rs73393812	1.00[AMR][1000 genomes]
rs73393831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393843	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25415000-25446200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:25416200-25441000	Weak transcription	Fetal Thymus	thymus
4	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
5	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:25418800-25462600	Weak transcription	Ovary	ovary
7	chr6:25420800-25441800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:25420800-25445400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:25421400-25442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:25421400-25446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:25421600-25446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25427000-25444400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:25432400-25445800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:25432400-25447800	Weak transcription	Gastric	stomach
15	chr6:25432600-25445400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:25433000-25442400	Weak transcription	Fetal Lung	lung
17	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:25433600-25442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:25434000-25446200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:25434200-25450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:25435800-25447800	Weak transcription	Lung	lung
22	chr6:25436000-25442200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:25436000-25443000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:25436000-25445400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:25436200-25441000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:25436200-25441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:25436600-25441600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:25436800-25443000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:25437000-25442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:25437000-25445800	Weak transcription	Fetal Intestine Large	intestine
32	chr6:25437400-25441400	Weak transcription	Aorta	Aorta
33	chr6:25437400-25445800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:25438400-25446400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:25438800-25442600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:25439400-25440600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:25439800-25440600	Strong transcription	NHEK	skin
39	chr6:25439800-25441200	Weak transcription	Thymus	Thymus
40	chr6:25440000-25446200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:25440000-25447800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:25440400-25440600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr6:25440400-25442000	Enhancers	Primary T cells from cord blood	blood
44	chr6:25440400-25443600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:25440400-25443600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr6:25440400-25443800	Enhancers	Primary T helper cells fromperipheralblood	blood

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