Variant report

Variant	rs10978680
Chromosome Location	chr9:109714870-109714871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:109714792..109715652-chr9:109893660..109894517,2	MCF-7	breast:
2	chr9:109479273..109482095-chr9:109712075..109715276,3	MCF-7	breast:
3	chr9:109624066..109626442-chr9:109713986..109715671,2	MCF-7	breast:
4	chr9:109714792..109715773-chr9:109893976..109894517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148143	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10512351	0.92[YRI][hapmap]
rs10978681	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10978682	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11790439	0.85[ASW][hapmap];0.92[YRI][hapmap]
rs12351612	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7848294	1.00[TSI][hapmap]
rs7868949	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869202	chr9:108940763-109811530	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv831680	chr9:109653596-109848827	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109686200-109722600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:109688600-109738600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:109690400-109728600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:109692000-109734200	Weak transcription	Colonic Mucosa	Colon
5	chr9:109695000-109715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:109698000-109721400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:109698000-109721600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:109698000-109722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:109699200-109719000	Weak transcription	Pancreas	Pancrea
10	chr9:109700800-109724000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:109701400-109729600	Weak transcription	Brain Angular Gyrus	brain
12	chr9:109702000-109717400	Weak transcription	Dnd41	blood
13	chr9:109702200-109732400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:109702400-109715000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:109702400-109715400	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:109702400-109720400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:109702400-109730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:109702400-109734200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr9:109702400-109734200	Weak transcription	Lung	lung
20	chr9:109702600-109718600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:109702600-109734200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:109703400-109715000	Weak transcription	Placenta	Placenta
23	chr9:109703600-109715000	Weak transcription	Ovary	ovary
24	chr9:109703600-109731800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:109703600-109734200	Weak transcription	Esophagus	oesophagus
26	chr9:109703600-109734200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:109703800-109729800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:109704600-109715400	Weak transcription	Right Ventricle	heart
29	chr9:109704600-109721000	Weak transcription	Right Atrium	heart
30	chr9:109704800-109717000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:109704800-109736400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:109705000-109715000	Weak transcription	HSMMtube	muscle
33	chr9:109705000-109716200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:109705200-109721400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:109706000-109722600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:109706400-109715400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:109707600-109728600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:109707800-109716800	Strong transcription	Fetal Intestine Large	intestine
39	chr9:109707800-109723400	Strong transcription	Fetal Lung	lung
40	chr9:109708400-109715000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:109708400-109730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:109708600-109718800	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:109708800-109718800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:109709600-109715200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:109709600-109715200	Weak transcription	NHDF-Ad	bronchial
46	chr9:109709600-109721000	Weak transcription	HUVEC	blood vessel
47	chr9:109709800-109715000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:109709800-109715200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:109709800-109715200	Weak transcription	NHLF	lung
50	chr9:109709800-109718600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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