Variant report

Variant	rs2394164
Chromosome Location	chr6:29721397-29721398
allele	C/G
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	RCOR1	chr6:29720327-29721498	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr6:29721260-29721410	NHEK	skin:	n/a	n/a
3	POLR2A	chr6:29721310-29721420	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr6:29720196-29721487	HCT-116	colon:	n/a	chr6:29720979-29720988 chr6:29721022-29721038 chr6:29720801-29720814

No.	Distal block	Cell Line	Cell type
1	chr6:29710119..29712623-chr6:29721345..29723379,2	MCF-7	breast:
2	chr6:29720902..29721504-chr6:29815550..29816084,2	K562	blood:
3	chr6:29719431..29722230-chr6:29728984..29731849,2	MCF-7	breast:
4	chr6:29720457..29721452-chr8:47957248..47957748,2	MCF-7	breast:
5	chr6:29709930..29711722-chr6:29720449..29722464,2	K562	blood:
6	chr6:29705500..29706511-chr6:29720185..29721437,3	K562	blood:
7	chr6:29716316..29718223-chr6:29719581..29721724,2	MCF-7	breast:

Variant related genes	Relation type
MICE	TF binding region
IFITM4P	TF binding region
ENSG00000272236	TF binding region
HLA-F-AS1	TF binding region
ENSG00000273340	Chromatin interaction
ENSG00000214922	Chromatin interaction
ENSG00000270896	Chromatin interaction
ENSG00000199290	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12665401	0.94[AFR][1000 genomes]
rs1610622	0.85[ASN][1000 genomes]
rs1610733	0.85[ASN][1000 genomes]
rs1610734	0.85[ASN][1000 genomes]
rs1610736	0.85[ASN][1000 genomes]
rs1623122	0.85[ASN][1000 genomes]
rs1633080	0.85[ASN][1000 genomes]
rs1633084	0.85[ASN][1000 genomes]
rs1633085	0.85[ASN][1000 genomes]
rs1633089	0.84[ASN][1000 genomes]
rs16867712	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1737083	0.85[ASN][1000 genomes]
rs1737085	0.84[ASN][1000 genomes]
rs17875376	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2523420	0.84[ASN][1000 genomes]
rs2523753	0.80[ASN][1000 genomes]
rs2523754	0.81[ASN][1000 genomes]
rs2735046	0.80[ASN][1000 genomes]
rs2743951	0.80[ASN][1000 genomes]
rs34260811	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4084764	0.86[EUR][1000 genomes]
rs4713237	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713239	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713240	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713242	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713244	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760145	0.84[ASN][1000 genomes]
rs7754067	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759474	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759482	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs909728	0.85[ASN][1000 genomes]
rs909729	0.84[ASN][1000 genomes]
rs9368609	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9391630	0.86[EUR][1000 genomes]
rs9391660	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription 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	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers 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

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29719600-29721400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:29719600-29721400	Active TSS	HSMM	muscle
3	chr6:29719600-29721400	Active TSS	NHDF-Ad	bronchial
4	chr6:29719600-29721800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:29719800-29721400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:29719800-29721600	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:29719800-29721600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:29719800-29721600	Active TSS	HSMMtube	muscle
9	chr6:29720000-29721400	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr6:29720000-29721400	Flanking Bivalent TSS/Enh	Dnd41	blood
11	chr6:29720200-29721400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:29720200-29721400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:29720200-29721400	Active TSS	HMEC	breast
14	chr6:29720200-29721400	Active TSS	K562	blood
15	chr6:29720200-29721600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:29720200-29721600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:29720200-29721600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:29720200-29721600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr6:29720400-29721400	Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:29720400-29721400	Active TSS	Hela-S3	cervix
21	chr6:29720400-29721600	Active TSS	Stomach Smooth Muscle	stomach
22	chr6:29720600-29721400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:29721000-29721400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:29721000-29721400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:29721000-29721400	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr6:29721000-29721600	Enhancers	Primary T cells from cord blood	blood
27	chr6:29721000-29721600	Bivalent Enhancer	Fetal Intestine Large	intestine
28	chr6:29721000-29721800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:29721000-29721800	Enhancers	Duodenum Mucosa	Duodenum
30	chr6:29721000-29723000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:29721000-29723200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:29721000-29723200	Weak transcription	Spleen	Spleen
33	chr6:29721000-29724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:29721000-29725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:29721200-29721400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:29721200-29721400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:29721200-29721400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr6:29721200-29721400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:29721200-29721400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:29721200-29721400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr6:29721200-29721400	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr6:29721200-29721400	Flanking Active TSS	HUVEC	blood vessel
43	chr6:29721200-29721400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr6:29721200-29721400	Flanking Active TSS	NHLF	lung
45	chr6:29721200-29721400	Enhancers	Osteobl	bone
46	chr6:29721200-29721600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:29721200-29721600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:29721200-29721600	Enhancers	Primary B cells from cord blood	blood
49	chr6:29721200-29721600	Enhancers	Primary B cells from peripheral blood	blood
50	chr6:29721200-29721600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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