Variant report

Variant	rs2744938
Chromosome Location	chr6:34552110-34552111
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34551284..34553223-chr6:34555958..34557670,2	MCF-7	breast:
2	chr6:34550788..34556388-chr6:34565460..34570894,5	K562	blood:
3	chr6:34522438..34524089-chr6:34549801..34552822,3	MCF-7	breast:
4	chr6:34535538..34537048-chr6:34550660..34552218,2	K562	blood:
5	chr6:34543493..34547191-chr6:34549783..34553774,3	MCF-7	breast:
6	chr6:34546025..34550946-chr6:34551862..34556143,7	K562	blood:
7	chr6:34543118..34546056-chr6:34551704..34553815,2	K562	blood:
8	chr6:34548787..34550337-chr6:34551862..34554295,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196114	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11752260	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2092344	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2492859	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2492863	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744937	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2744942	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2744947	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2744954	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2744955	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2744956	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2744964	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744965	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2744971	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2744972	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2744977	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814943	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814948	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814973	0.94[EUR][1000 genomes]
rs2814977	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2814983	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814985	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814986	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814993	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814994	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2814996	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815005	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3800457	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56930444	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9469860	0.82[EUR][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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv516578	chr6:34483015-34561585	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1032763	chr6:34509776-34552797	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv1025472	chr6:34509776-34555969	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv1033534	chr6:34516588-34555969	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
12	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv823667	chr6:34533015-34592524	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv818410	chr6:34538544-34579431	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	esv988873	chr6:34548881-34557080	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2744938	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2744938	C6orf106	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34535600-34563200	Weak transcription	A549	lung
2	chr6:34536800-34554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:34536800-34556600	Weak transcription	Hela-S3	cervix
4	chr6:34537400-34552800	Weak transcription	Fetal Intestine Large	intestine
5	chr6:34538000-34555400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:34538800-34552600	Weak transcription	Right Ventricle	heart
7	chr6:34539600-34552800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:34540800-34554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:34541600-34553200	Weak transcription	Lung	lung
10	chr6:34541800-34553400	Weak transcription	HepG2	liver
11	chr6:34542000-34553000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:34542200-34555400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:34542400-34553800	Weak transcription	Liver	Liver
14	chr6:34543200-34552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:34544200-34555000	Weak transcription	Pancreas	Pancrea
16	chr6:34544600-34553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:34544600-34553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:34545000-34554400	Weak transcription	NHEK	skin
19	chr6:34545200-34552600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:34545200-34552800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:34545400-34554000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:34545800-34552600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:34545800-34553200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:34546000-34554000	Weak transcription	Fetal Thymus	thymus
25	chr6:34546000-34559800	Weak transcription	HSMM	muscle
26	chr6:34546200-34553000	Weak transcription	K562	blood
27	chr6:34546400-34555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:34546600-34552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:34546600-34552600	Weak transcription	Gastric	stomach
30	chr6:34546600-34553000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:34546600-34553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:34546800-34552400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:34547200-34553200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:34547200-34555600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:34547200-34566800	Weak transcription	Aorta	Aorta
36	chr6:34547400-34553400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr6:34547600-34555400	Weak transcription	Primary B cells from cord blood	blood
38	chr6:34547800-34554200	Weak transcription	Dnd41	blood
39	chr6:34548200-34553000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:34548200-34554800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:34548400-34552600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:34548600-34553000	Weak transcription	GM12878-XiMat	blood
43	chr6:34548800-34555400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:34548800-34561400	Weak transcription	Fetal Heart	heart
45	chr6:34549000-34552600	Weak transcription	Brain Anterior Caudate	brain
46	chr6:34549000-34555000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:34549000-34555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:34549000-34564200	Strong transcription	Fetal Intestine Small	intestine
49	chr6:34549200-34552600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:34549200-34553000	Weak transcription	Brain Hippocampus Middle	brain

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