Variant report

Variant	rs3893399
Chromosome Location	chr9:86046077-86046078
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	chr9:86045543..86047511-chr9:86062619..86064900,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10217271	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10217435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10217669	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10217746	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10217752	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140068	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140071	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140080	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140081	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140082	0.85[MEX][hapmap]
rs11140083	0.81[MEX][hapmap]
rs11140085	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11998876	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12000173	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12005884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337733	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12339003	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12340422	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs12346296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12350642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12551179	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12553050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17086251	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4636280	0.84[MEX][hapmap]
rs4877758	0.84[MEX][hapmap]
rs4877767	0.90[MEX][hapmap]
rs61424289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7023220	0.90[MEX][hapmap]
rs73465724	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73465767	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181122	0.94[MEX][hapmap]

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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1048086	chr9:86040900-86059732	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3893399	HNRNPK	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86037800-86047200	Weak transcription	Fetal Stomach	stomach
2	chr9:86038400-86046600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:86040200-86046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:86040400-86050000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:86041800-86046600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:86041800-86046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:86041800-86047000	Weak transcription	Brain Angular Gyrus	brain
9	chr9:86042200-86046600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:86042200-86046800	Weak transcription	Lung	lung
11	chr9:86042400-86046600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:86044000-86047600	Enhancers	Pancreas	Pancrea
13	chr9:86044400-86047600	Enhancers	Left Ventricle	heart
14	chr9:86044800-86046800	Enhancers	HepG2	liver
15	chr9:86045000-86046200	Enhancers	Fetal Muscle Trunk	muscle
16	chr9:86045000-86047600	Enhancers	Fetal Muscle Leg	muscle
17	chr9:86045200-86046800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:86045400-86046600	Enhancers	A549	lung
19	chr9:86045600-86046200	Enhancers	Gastric	stomach
20	chr9:86045600-86046400	Enhancers	Fetal Brain Male	brain
21	chr9:86045600-86046600	Enhancers	Stomach Smooth Muscle	stomach
22	chr9:86045600-86047000	Enhancers	Adipose Nuclei	Adipose
23	chr9:86045600-86047400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:86045600-86047600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:86045600-86047600	Enhancers	Aorta	Aorta
26	chr9:86045600-86047600	Enhancers	Colon Smooth Muscle	Colon
27	chr9:86045600-86047600	Enhancers	Ovary	ovary
28	chr9:86045600-86047600	Enhancers	Right Atrium	heart
29	chr9:86045600-86048200	Enhancers	Liver	Liver
30	chr9:86045800-86046200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:86045800-86046200	Enhancers	Brain Hippocampus Middle	brain
32	chr9:86045800-86046600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:86045800-86046600	Enhancers	Hela-S3	cervix
34	chr9:86045800-86046800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr9:86045800-86047400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:86045800-86047400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:86045800-86047400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr9:86045800-86047400	Enhancers	Fetal Lung	lung
39	chr9:86045800-86047400	Enhancers	HSMMtube	muscle
40	chr9:86045800-86047600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:86045800-86047600	Enhancers	Psoas Muscle	Psoas
42	chr9:86045800-86047600	Enhancers	Spleen	Spleen
43	chr9:86045800-86048000	Enhancers	NHDF-Ad	bronchial
44	chr9:86045800-86048200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr9:86046000-86046400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:86046000-86046400	Weak transcription	Small Intestine	intestine
47	chr9:86046000-86046600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:86046000-86046800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:86046000-86047000	Enhancers	Duodenum Mucosa	Duodenum
50	chr9:86046000-86047400	Enhancers	Right Ventricle	heart

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