Variant report

Variant	rs2486409
Chromosome Location	chr6:149401466-149401467
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:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149364667..149368591-chr6:149398600..149403391,5	MCF-7	breast:
2	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:
3	chr6:149399566..149401649-chr6:149452459..149454867,2	MCF-7	breast:
4	chr6:149399709..149402380-chr6:149772394..149774498,2	K562	blood:
5	chr6:149401238..149401748-chr6:149748753..149749409,2	MCF-7	breast:
6	chr6:149401082..149403539-chr6:149632212..149635956,4	MCF-7	breast:
7	chr6:149351961..149352960-chr6:149401183..149401797,2	MCF-7	breast:
8	chr6:149400077..149402541-chr6:149553088..149555803,2	MCF-7	breast:
9	chr6:149353519..149354505-chr6:149400647..149401590,2	MCF-7	breast:
10	chr6:149358004..149360292-chr6:149400901..149403577,2	MCF-7	breast:
11	chr6:149398184..149404330-chr6:149748783..149757211,17	MCF-7	breast:
12	chr6:149381811..149382908-chr6:149401148..149401993,4	MCF-7	breast:
13	chr6:149353741..149354649-chr6:149401105..149401931,5	MCF-7	breast:
14	chr6:149400690..149404463-chr6:149557705..149560765,3	MCF-7	breast:
15	chr6:149400971..149403372-chr6:149403878..149405547,2	K562	blood:
16	chr6:149353100..149353685-chr6:149401323..149401899,2	MCF-7	breast:
17	chr6:149400900..149408936-chr6:149636750..149640736,16	MCF-7	breast:
18	chr6:149340644..149342659-chr6:149400805..149403044,2	MCF-7	breast:
19	chr6:149350906..149355297-chr6:149396132..149403444,27	MCF-7	breast:
20	chr6:149393800..149396694-chr6:149401142..149403800,2	K562	blood:
21	chr6:148954816..148955529-chr6:149401033..149401601,2	MCF-7	breast:
22	chr6:149401028..149403801-chr6:149413849..149415930,2	MCF-7	breast:
23	chr6:149353980..149354853-chr6:149401096..149401673,2	MCF-7	breast:
24	chr6:149068413..149070545-chr6:149400002..149402666,2	MCF-7	breast:
25	chr6:149381811..149382802-chr6:149401148..149401945,4	MCF-7	breast:
26	chr6:149393614..149396694-chr6:149401142..149403800,3	K562	blood:
27	chr6:148954756..148955529-chr6:149401033..149401756,3	MCF-7	breast:
28	chr6:149353945..149354680-chr6:149401078..149401622,2	MCF-7	breast:
29	chr6:149401024..149403693-chr6:149738152..149741655,3	K562	blood:
30	chr6:149401238..149401990-chr6:149748324..149749629,5	MCF-7	breast:
31	chr6:149400434..149403081-chr6:149638090..149639793,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111962	Chromatin interaction
ENSG00000055208	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2340798	0.81[CEU][hapmap]
rs2486411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2500549	0.82[CEU][hapmap]
rs6904550	0.84[CEU][hapmap]
rs6931675	0.83[GIH][hapmap]
rs6935330	0.81[TSI][hapmap]
rs7748978	0.85[CEU][hapmap]
rs7774457	0.85[CEU][hapmap]
rs9285516	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9377188	0.85[CEU][hapmap]
rs9399678	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2486409	C6orf97	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149385200-149404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:149387400-149404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:149387600-149401800	Weak transcription	Brain Substantia Nigra	brain
4	chr6:149395000-149415000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:149396800-149403400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:149397400-149402200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:149397400-149403400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:149397400-149403600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:149397600-149403600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:149397800-149401600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:149397800-149407600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149398600-149401600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:149398600-149403200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:149398800-149402800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:149398800-149403800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:149399000-149402400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:149399000-149403200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:149399000-149403200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:149399000-149403200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:149399000-149403600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:149399200-149415000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:149399800-149402200	Enhancers	Right Atrium	heart
23	chr6:149399800-149403000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:149400000-149402800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:149400200-149401600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:149400200-149402200	Enhancers	Ovary	ovary
27	chr6:149400200-149403000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:149400200-149406000	Enhancers	Dnd41	blood
29	chr6:149400400-149401800	Enhancers	Stomach Smooth Muscle	stomach
30	chr6:149400400-149402200	Enhancers	Fetal Muscle Leg	muscle
31	chr6:149400400-149402200	Enhancers	Fetal Thymus	thymus
32	chr6:149400400-149402200	Enhancers	HSMMtube	muscle
33	chr6:149400400-149402400	Enhancers	Fetal Stomach	stomach
34	chr6:149400400-149402400	Enhancers	HepG2	liver
35	chr6:149400400-149402600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:149400400-149402800	Enhancers	NHLF	lung
37	chr6:149400400-149403000	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:149400400-149403200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:149400400-149403400	Enhancers	Osteobl	bone
40	chr6:149400600-149401600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:149400600-149401600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:149400600-149401800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:149400600-149402000	Enhancers	NHEK	skin
44	chr6:149400600-149402200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:149400600-149402200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:149400600-149402200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:149400600-149402200	Enhancers	Adipose Nuclei	Adipose
48	chr6:149400600-149402200	Enhancers	Fetal Muscle Trunk	muscle
49	chr6:149400600-149402200	Enhancers	Left Ventricle	heart
50	chr6:149400600-149402200	Enhancers	Pancreas	Pancrea

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