Variant report

Variant	rs394199
Chromosome Location	chr6:33553580-33553581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33553322..33554036-chr6:33667998..33668833,3	MCF-7	breast:
2	chr6:33553164..33555974-chr6:33639876..33642136,2	MCF-7	breast:
3	chr6:33551460..33554975-chr6:33588078..33592105,4	K562	blood:
4	chr6:33553081..33555328-chr6:33667772..33669168,10	K562	blood:
5	chr6:33550022..33555745-chr6:33586647..33590467,5	MCF-7	breast:
6	chr6:33551901..33555908-chr6:33676752..33679381,5	K562	blood:
7	chr6:33553176..33554214-chr6:33667921..33668866,4	MCF-7	breast:
8	chr6:33552057..33555351-chr6:33600748..33604007,3	MCF-7	breast:
9	chr6:33553409..33554021-chr6:34122638..34123185,2	K562	blood:
10	chr6:33384196..33386645-chr6:33552574..33554724,2	MCF-7	breast:
11	chr6:33551917..33554088-chr6:33585146..33588477,3	K562	blood:
12	chr6:33384739..33386700-chr6:33551719..33554109,2	MCF-7	breast:
13	chr6:33553147..33553827-chr6:33730088..33730602,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112514	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs210137	0.87[CHB][hapmap]
rs210138	0.87[CHB][hapmap]
rs375555	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs395671	0.81[JPT][hapmap]
rs493871	0.86[CHD][hapmap]
rs530878	0.82[CHB][hapmap]
rs563751	0.82[CHB][hapmap]
rs6900408	0.81[CHB][hapmap]
rs6929774	0.87[GIH][hapmap]

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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs394199	C6orf106	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33548400-33553600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:33548400-33553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:33548400-33553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:33548400-33553600	Weak transcription	Brain Germinal Matrix	brain
5	chr6:33548400-33553600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:33548400-33553600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:33548400-33553600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:33548400-33557000	Weak transcription	HSMM	muscle
9	chr6:33548400-33557200	Weak transcription	NHDF-Ad	bronchial
10	chr6:33548400-33557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:33548400-33557800	Weak transcription	Right Atrium	heart
12	chr6:33548600-33553600	Weak transcription	Osteobl	bone
13	chr6:33548600-33560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:33548800-33553600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:33548800-33557800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33551800-33557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33552000-33557000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:33552400-33554200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:33552400-33554200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:33552600-33553600	Enhancers	GM12878-XiMat	blood
21	chr6:33552600-33554000	Enhancers	Primary T cells from cord blood	blood
22	chr6:33552600-33554000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:33552600-33554000	Enhancers	NHEK	skin
24	chr6:33552600-33554600	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:33552800-33553600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:33552800-33554000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:33552800-33554000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:33552800-33554000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:33552800-33554000	Flanking Active TSS	Dnd41	blood
30	chr6:33552800-33554200	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:33552800-33554200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:33553000-33553600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:33553000-33553600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr6:33553000-33553800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:33553000-33553800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:33553000-33553800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33553000-33554000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:33553000-33554000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:33553000-33554000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:33553000-33554000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:33553000-33554200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:33553000-33554200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:33553000-33554200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:33553000-33554200	Enhancers	Fetal Muscle Trunk	muscle
45	chr6:33553000-33554400	Enhancers	Primary B cells from cord blood	blood
46	chr6:33553000-33554800	Enhancers	Spleen	Spleen
47	chr6:33553200-33553600	Enhancers	Brain Angular Gyrus	brain
48	chr6:33553200-33553800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr6:33553200-33553800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:33553200-33553800	Enhancers	Esophagus	oesophagus

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