Variant report

Variant	rs7863447
Chromosome Location	chr9:14155418-14155419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14152718..14156073-chr9:14313268..14315802,3	MCF-7	breast:
2	chr9:14149670..14153265-chr9:14153637..14156329,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10511592	0.92[CEU][hapmap]
rs10756531	0.86[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10810105	1.00[YRI][hapmap]
rs10810108	1.00[YRI][hapmap]
rs10810109	1.00[YRI][hapmap]
rs10961412	1.00[YRI][hapmap]
rs12156460	1.00[YRI][hapmap]
rs12349255	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12552654	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13300925	0.84[CEU][hapmap]
rs4237133	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4375095	1.00[YRI][hapmap]
rs4740559	0.84[CEU][hapmap]
rs6474820	0.84[CEU][hapmap]
rs7028001	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7031735	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs7042127	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs7042365	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7044402	0.92[CEU][hapmap]
rs7045411	0.84[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs723968	0.92[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7868947	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv892595	chr9:14129951-14168029	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv892596	chr9:14145487-14208724	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7863447	BNC2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14116600-14159200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:14116600-14179200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:14116800-14156000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:14117000-14171200	Weak transcription	Hela-S3	cervix
5	chr9:14120200-14159000	Weak transcription	NHLF	lung
6	chr9:14120600-14159000	Weak transcription	NH-A	brain
7	chr9:14123800-14198600	Weak transcription	Gastric	stomach
8	chr9:14127000-14156400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:14131800-14173200	Weak transcription	Pancreas	Pancrea
10	chr9:14134000-14181000	Weak transcription	Ovary	ovary
11	chr9:14134200-14156200	Weak transcription	Right Ventricle	heart
12	chr9:14134200-14159400	Weak transcription	Fetal Stomach	stomach
13	chr9:14142200-14159000	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:14144000-14157000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:14144400-14156400	Weak transcription	Brain Substantia Nigra	brain
16	chr9:14145000-14159400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:14146800-14159000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:14147200-14156400	Weak transcription	Liver	Liver
19	chr9:14148000-14156200	Weak transcription	Right Atrium	heart
20	chr9:14149200-14159000	Weak transcription	Osteobl	bone
21	chr9:14151800-14159000	Weak transcription	Aorta	Aorta
22	chr9:14152000-14156000	Weak transcription	Left Ventricle	heart
23	chr9:14152600-14159200	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:14153600-14156400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:14153600-14156400	Weak transcription	Psoas Muscle	Psoas
26	chr9:14153600-14156600	Weak transcription	Small Intestine	intestine
27	chr9:14153600-14156800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:14153600-14156800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:14153600-14158600	Weak transcription	NHDF-Ad	bronchial
30	chr9:14153600-14159000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:14153600-14159000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:14153600-14159600	Weak transcription	Fetal Brain Female	brain
33	chr9:14153600-14159600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:14153800-14156200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:14153800-14156600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:14153800-14157200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr9:14153800-14158200	Weak transcription	A549	lung
38	chr9:14153800-14159000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:14153800-14159200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr9:14154200-14155600	Strong transcription	Fetal Muscle Leg	muscle
41	chr9:14154200-14157200	Enhancers	Primary hematopoietic stem cells	blood
42	chr9:14154400-14156400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:14154400-14157200	Enhancers	Fetal Heart	heart
44	chr9:14154600-14155600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:14154600-14157400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:14154800-14156600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:14155000-14155600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:14155000-14155600	Enhancers	Adipose Nuclei	Adipose
49	chr9:14155000-14155600	Strong transcription	Brain Germinal Matrix	brain
50	chr9:14155000-14155600	Enhancers	Skeletal Muscle Male	skeletal muscle

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