Variant report

Variant	rs7770540
Chromosome Location	chr6:149382031-149382032
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149380842..149383187-chr6:149749461..149751628,2	MCF-7	breast:
2	chr6:149356091..149358662-chr6:149380682..149383777,5	MCF-7	breast:
3	chr6:149381576..149384224-chr6:149749932..149753109,3	MCF-7	breast:
4	chr6:149347925..149355177-chr6:149378699..149385191,19	MCF-7	breast:
5	chr6:149367003..149368694-chr6:149381006..149384562,3	K562	blood:
6	chr6:149381811..149382908-chr6:149401148..149401993,4	MCF-7	breast:
7	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:
8	chr6:149379361..149382289-chr6:149745014..149748004,4	MCF-7	breast:
9	chr6:149376538..149378181-chr6:149380080..149383036,2	K562	blood:
10	chr6:149380086..149382702-chr6:149642964..149645035,2	MCF-7	breast:
11	chr6:149364981..149368017-chr6:149381154..149384452,3	MCF-7	breast:
12	chr6:149352329..149353452-chr6:149381767..149382867,3	MCF-7	breast:
13	chr6:149345224..149347260-chr6:149380450..149382499,2	MCF-7	breast:
14	chr6:149381088..149383058-chr6:149414648..149416261,2	MCF-7	breast:
15	chr6:149373800..149377779-chr6:149379783..149384195,7	MCF-7	breast:
16	chr6:149381811..149382802-chr6:149401148..149401945,4	MCF-7	breast:
17	chr6:149380862..149385743-chr6:149637114..149641554,7	MCF-7	breast:
18	chr6:149378324..149381149-chr6:149381718..149384310,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17081680	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55816736	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55976567	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57237482	1.00[EUR][1000 genomes]
rs58229843	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58877156	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58924506	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61173696	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6909521	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6928184	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73599932	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73599942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73599945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7740389	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7750481	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7752650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7757287	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9485350	0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9498192	1.00[AMR][1000 genomes]

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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:149359200-149383600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:149362600-149385200	Weak transcription	Aorta	Aorta
4	chr6:149362800-149401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:149363200-149394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:149369000-149398800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:149371400-149396400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:149371800-149397000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:149375800-149384000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:149379200-149383400	Enhancers	Fetal Lung	lung
11	chr6:149379200-149385000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149379400-149384200	Enhancers	Placenta	Placenta
13	chr6:149379400-149388600	Enhancers	Fetal Thymus	thymus
14	chr6:149380000-149383200	Enhancers	Fetal Kidney	kidney
15	chr6:149380200-149382400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:149380200-149382400	Enhancers	Fetal Muscle Trunk	muscle
17	chr6:149380200-149382800	Enhancers	Fetal Muscle Leg	muscle
18	chr6:149380200-149383000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:149380200-149383000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:149380200-149384000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:149380200-149386000	Enhancers	HSMMtube	muscle
22	chr6:149380400-149382600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:149380400-149383200	Enhancers	NH-A	brain
24	chr6:149380400-149385800	Enhancers	HSMM	muscle
25	chr6:149380400-149386600	Enhancers	GM12878-XiMat	blood
26	chr6:149380800-149382200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:149380800-149383000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:149380800-149387400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:149380800-149388400	Enhancers	Fetal Stomach	stomach
30	chr6:149380800-149396200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:149381000-149382200	Weak transcription	Brain Substantia Nigra	brain
32	chr6:149381000-149382400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr6:149381000-149382800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:149381000-149382800	Enhancers	Thymus	Thymus
35	chr6:149381000-149383200	Enhancers	Fetal Intestine Small	intestine
36	chr6:149381000-149385400	Flanking Active TSS	Dnd41	blood
37	chr6:149381000-149394800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:149381000-149395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:149381200-149382600	Enhancers	NHLF	lung
40	chr6:149381200-149383800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:149381200-149385400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:149381400-149382200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:149381400-149382200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr6:149381400-149382200	Enhancers	Colon Smooth Muscle	Colon
45	chr6:149381400-149382200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr6:149381400-149382200	Enhancers	Stomach Smooth Muscle	stomach
47	chr6:149381400-149382200	Enhancers	Spleen	Spleen
48	chr6:149381400-149382600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:149381400-149382600	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:149381400-149382800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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