Variant report

Variant	rs2841560
Chromosome Location	chr6:13462198-13462199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13459869..13463008-chr6:13572189..13575188,3	MCF-7	breast:
2	chr6:13461624..13463147-chr6:13573549..13575952,2	MCF-7	breast:
3	chr6:13461316..13464526-chr6:13474276..13478535,4	MCF-7	breast:
4	chr6:13458780..13460333-chr6:13460354..13463119,2	MCF-7	breast:
5	chr6:13460797..13463308-chr6:13464460..13467196,3	K562	blood:
6	chr6:13453259..13455801-chr6:13460525..13463218,2	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2560757	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2560759	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2560761	1.00[ASN][1000 genomes]
rs2841564	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62385775	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13438600-13462200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13452200-13483400	Weak transcription	Gastric	stomach
3	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
4	chr6:13455200-13462600	Weak transcription	Stomach Mucosa	stomach
5	chr6:13455200-13466600	Weak transcription	Pancreas	Pancrea
6	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
7	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:13455400-13462600	Weak transcription	HSMM	muscle
9	chr6:13455400-13463200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
11	chr6:13456200-13463000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:13456200-13463000	Weak transcription	Fetal Brain Female	brain
13	chr6:13456200-13464400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:13456200-13466200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:13456600-13467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:13457800-13462200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:13457800-13462400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:13458200-13462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:13458200-13462200	Weak transcription	Fetal Brain Male	brain
20	chr6:13458200-13462200	Weak transcription	HMEC	breast
21	chr6:13458200-13462600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:13458200-13462600	Weak transcription	NH-A	brain
23	chr6:13458200-13462800	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:13458200-13463000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:13458200-13465600	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:13458200-13465800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:13458200-13466000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:13458200-13466000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:13458200-13466600	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:13458400-13462800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:13458400-13462800	Weak transcription	Fetal Stomach	stomach
32	chr6:13458400-13466200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:13458600-13463200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:13459000-13466200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:13459400-13463000	Weak transcription	Fetal Heart	heart
36	chr6:13459400-13463000	Weak transcription	Psoas Muscle	Psoas
37	chr6:13460400-13462200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:13460400-13462200	Weak transcription	Hela-S3	cervix
39	chr6:13461000-13463400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:13461200-13462600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:13461200-13463400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:13461200-13464600	Enhancers	Right Atrium	heart
43	chr6:13461200-13465200	Enhancers	Fetal Lung	lung
44	chr6:13461400-13462400	Strong transcription	Aorta	Aorta
45	chr6:13461400-13462400	Enhancers	Lung	lung
46	chr6:13461400-13463000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:13461400-13463200	Genic enhancers	Right Ventricle	heart
48	chr6:13461400-13463200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:13461400-13463400	Genic enhancers	Spleen	Spleen
50	chr6:13461400-13463600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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