Variant report

Variant	rs723968
Chromosome Location	chr9:14154231-14154232
allele	C/T
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]
rs10511591	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10511592	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12004755	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs12552654	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12554151	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13300925	0.90[AFR][1000 genomes]
rs16931403	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237133	0.85[CEU][hapmap]
rs4740559	0.82[AFR][1000 genomes]
rs6474820	0.81[JPT][hapmap]
rs7028001	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029562	0.86[CEU][hapmap]
rs7030475	0.86[CEU][hapmap]
rs7031735	0.92[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7042127	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs7042365	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7044402	0.85[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs7045411	0.92[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73642095	0.85[ASN][1000 genomes]
rs73642097	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7863447	0.92[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7868947	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]

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
rs723968	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	chr9:14120600-14154800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:14120600-14159000	Weak transcription	NH-A	brain
8	chr9:14123800-14198600	Weak transcription	Gastric	stomach
9	chr9:14127000-14156400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:14131800-14173200	Weak transcription	Pancreas	Pancrea
11	chr9:14134000-14181000	Weak transcription	Ovary	ovary
12	chr9:14134200-14156200	Weak transcription	Right Ventricle	heart
13	chr9:14134200-14159400	Weak transcription	Fetal Stomach	stomach
14	chr9:14136000-14155000	Weak transcription	Brain Germinal Matrix	brain
15	chr9:14142200-14159000	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:14144000-14157000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:14144400-14155000	Weak transcription	Brain Angular Gyrus	brain
18	chr9:14144400-14156400	Weak transcription	Brain Substantia Nigra	brain
19	chr9:14145000-14159400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:14145600-14155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:14146800-14154400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:14146800-14159000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:14147000-14154400	Weak transcription	HSMM	muscle
24	chr9:14147200-14156400	Weak transcription	Liver	Liver
25	chr9:14148000-14156200	Weak transcription	Right Atrium	heart
26	chr9:14149000-14155000	Weak transcription	NHEK	skin
27	chr9:14149200-14159000	Weak transcription	Osteobl	bone
28	chr9:14150200-14154400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr9:14150400-14154400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:14151800-14159000	Weak transcription	Aorta	Aorta
31	chr9:14152000-14154600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:14152000-14156000	Weak transcription	Left Ventricle	heart
33	chr9:14152600-14159200	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:14153200-14155000	Enhancers	HUVEC	blood vessel
35	chr9:14153400-14154400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:14153400-14154400	Weak transcription	Fetal Kidney	kidney
37	chr9:14153400-14155200	Enhancers	HMEC	breast
38	chr9:14153600-14154400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:14153600-14154600	Weak transcription	Stomach Mucosa	stomach
40	chr9:14153600-14155000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:14153600-14156400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr9:14153600-14156400	Weak transcription	Psoas Muscle	Psoas
43	chr9:14153600-14156600	Weak transcription	Small Intestine	intestine
44	chr9:14153600-14156800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr9:14153600-14156800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:14153600-14158600	Weak transcription	NHDF-Ad	bronchial
47	chr9:14153600-14159000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr9:14153600-14159000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:14153600-14159600	Weak transcription	Fetal Brain Female	brain
50	chr9:14153600-14159600	Weak transcription	Rectal Smooth Muscle	rectum

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