Variant report

Variant	rs62400786
Chromosome Location	chr6:24701941-24701942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24700062..24702859-chr6:24704909..24709163,3	MCF-7	breast:
2	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
3	chr6:24530783..24533712-chr6:24700418..24704307,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf62-1	chr6:24701135-24702021	ENSG00000272345.1

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction
ENSG00000272402	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11559067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889567	1.00[ASN][1000 genomes]
rs17243136	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17243276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17412874	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17419844	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491730	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212238	1.00[ASN][1000 genomes]
rs62400556	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62400558	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62400559	1.00[ASN][1000 genomes]
rs62400760	1.00[ASN][1000 genomes]
rs62400773	1.00[ASN][1000 genomes]
rs62400774	1.00[ASN][1000 genomes]
rs62400783	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400789	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400790	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400791	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62400792	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400793	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400795	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400819	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400821	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62400822	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62402860	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62402864	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
2	chr6:24674800-24702200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24674800-24702200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:24674800-24702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:24676600-24702600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:24678200-24702600	Weak transcription	HSMMtube	muscle
7	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
8	chr6:24680600-24702600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:24681200-24705600	Weak transcription	Ovary	ovary
10	chr6:24682400-24703000	Weak transcription	Lung	lung
11	chr6:24682800-24702200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:24682800-24702200	Weak transcription	Fetal Stomach	stomach
13	chr6:24683000-24702200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:24684800-24705400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:24684800-24705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:24684800-24709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:24685800-24703600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:24686200-24703000	Weak transcription	HSMM	muscle
19	chr6:24686200-24703400	Weak transcription	Fetal Kidney	kidney
20	chr6:24687600-24703000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24687600-24703400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:24688000-24704000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:24691000-24703200	Weak transcription	Spleen	Spleen
24	chr6:24692400-24702000	Weak transcription	NHEK	skin
25	chr6:24692400-24702600	Weak transcription	Psoas Muscle	Psoas
26	chr6:24692600-24702400	Weak transcription	Right Ventricle	heart
27	chr6:24692800-24702200	Weak transcription	Left Ventricle	heart
28	chr6:24693200-24703000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:24693400-24702000	Weak transcription	Fetal Brain Female	brain
30	chr6:24693600-24702400	Weak transcription	Thymus	Thymus
31	chr6:24693600-24704000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:24693600-24705200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:24693800-24703000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:24695800-24702600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:24696200-24703000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:24696200-24703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:24696600-24704200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:24696600-24710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:24696800-24702200	Weak transcription	NHLF	lung
40	chr6:24696800-24703000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:24697200-24703200	Weak transcription	NHDF-Ad	bronchial
42	chr6:24697800-24703000	Weak transcription	Small Intestine	intestine
43	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
44	chr6:24698000-24703400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
46	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:24698400-24704000	Weak transcription	Hela-S3	cervix

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