Variant report

Variant	rs2235419
Chromosome Location	chr6:11728863-11728864
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:11728399-11729013	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ADTRP	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2235418	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2294419	0.80[AMR][1000 genomes]
rs2294421	0.80[AMR][1000 genomes]
rs2294425	0.81[AMR][1000 genomes]
rs2294426	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294427	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2294428	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713834	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4713849	0.81[AMR][1000 genomes]
rs760789	0.81[AMR][1000 genomes]
rs932345	0.83[EUR][1000 genomes]
rs9348963	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366877	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9368855	0.82[AMR][1000 genomes]
rs9394285	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462637	chr6:11710554-11733777	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600990	chr6:11710554-11733777	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235419	C6orf105	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11710800-11731000	Weak transcription	Gastric	stomach
2	chr6:11711200-11731000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:11711600-11731800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:11714600-11731600	Weak transcription	Small Intestine	intestine
5	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
6	chr6:11719600-11732400	Weak transcription	NHEK	skin
7	chr6:11723200-11731600	Strong transcription	HSMM	muscle
8	chr6:11723200-11732400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:11723200-11738400	Weak transcription	HMEC	breast
10	chr6:11723600-11744200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:11723800-11730600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:11723800-11731000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:11725200-11748600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:11725400-11731000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:11726200-11731000	Weak transcription	Fetal Intestine Large	intestine
16	chr6:11726400-11744600	Weak transcription	Right Atrium	heart
17	chr6:11727000-11730200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:11727000-11734000	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:11727400-11729200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:11727600-11729000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:11727600-11731000	Weak transcription	HSMMtube	muscle
22	chr6:11727600-11731800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:11727800-11729200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:11727800-11732800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:11728000-11730000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:11728000-11730200	Enhancers	Fetal Thymus	thymus
27	chr6:11728200-11731000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:11728400-11729000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:11728400-11729200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:11728400-11729200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:11728400-11729200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:11728400-11729400	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:11728400-11729600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr6:11728400-11729600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr6:11728400-11729600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:11728400-11729800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr6:11728400-11730000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr6:11728400-11730000	Enhancers	K562	blood
39	chr6:11728400-11731200	Enhancers	GM12878-XiMat	blood
40	chr6:11728600-11729400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr6:11728600-11729800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:11728600-11731200	Weak transcription	Spleen	Spleen
43	chr6:11728800-11729200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:11728800-11729200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr6:11728800-11729800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:11728800-11730000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:11728800-11730200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr6:11728800-11732400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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