Variant report

Variant	rs11097028
Chromosome Location	chr4:85869783-85869784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:85868885..85870740-chr4:85874876..85876493,2	MCF-7	breast:
2	chr14:91205640..91206160-chr4:85869406..85869926,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10856852	0.86[JPT][hapmap];0.86[TSI][hapmap]
rs11097026	0.81[CEU][hapmap]
rs11730981	0.81[EUR][1000 genomes]
rs12500519	0.89[EUR][1000 genomes]
rs12501525	0.92[AMR][1000 genomes]
rs12502409	0.82[EUR][1000 genomes]
rs12502559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503215	0.82[EUR][1000 genomes]
rs12503330	0.88[EUR][1000 genomes]
rs12506456	0.82[EUR][1000 genomes]
rs12510410	0.83[EUR][1000 genomes]
rs12648852	0.81[EUR][1000 genomes]
rs13109918	0.81[EUR][1000 genomes]
rs13118671	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13125323	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13139541	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13141072	0.87[EUR][1000 genomes]
rs1484661	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1508670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009317	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17009334	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17009341	0.81[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2046404	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs35190829	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35892581	0.94[EUR][1000 genomes]
rs4376130	0.82[EUR][1000 genomes]
rs4383611	1.00[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4533765	0.86[JPT][hapmap];0.86[TSI][hapmap]
rs4590017	1.00[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4624645	0.82[EUR][1000 genomes]
rs55871210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55912355	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56094216	0.90[EUR][1000 genomes]
rs58074983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531777	0.81[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs6531782	0.86[JPT][hapmap];0.86[TSI][hapmap]
rs6531783	0.93[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66965560	0.85[EUR][1000 genomes]
rs67624868	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815917	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6820517	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829807	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes]
rs6847564	0.94[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6847811	0.83[EUR][1000 genomes]
rs71631375	0.91[EUR][1000 genomes]
rs72664928	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72664957	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7654035	0.81[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs7661609	0.81[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7663580	0.86[JPT][hapmap];0.86[TSI][hapmap]
rs7682896	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7690054	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7692223	0.90[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7694949	0.81[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7695054	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7699226	0.81[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9684737	0.82[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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11097028	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:85809000-85872800	Weak transcription	A549	lung
3	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:85849200-85876000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85851200-85876000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:85860600-85872800	Weak transcription	Esophagus	oesophagus
7	chr4:85860600-85877000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:85860800-85872800	Weak transcription	NH-A	brain
9	chr4:85861200-85872400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:85861200-85873600	Weak transcription	HUVEC	blood vessel
11	chr4:85863400-85872600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:85864200-85872800	Weak transcription	HSMM	muscle
13	chr4:85864400-85873200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:85864400-85876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:85864400-85877200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:85864800-85870800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:85864800-85871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:85865200-85876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:85866400-85872000	Weak transcription	HMEC	breast
23	chr4:85866400-85872800	Weak transcription	Pancreas	Pancrea
24	chr4:85866400-85873200	Weak transcription	NHLF	lung
25	chr4:85866400-85879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:85866600-85873200	Weak transcription	Osteobl	bone
27	chr4:85866800-85870200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:85866800-85871600	Weak transcription	Lung	lung
29	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:85867200-85869800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:85867800-85869800	Weak transcription	Right Ventricle	heart
32	chr4:85867800-85878600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:85868800-85869800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:85868800-85869800	Enhancers	Placenta	Placenta
35	chr4:85868800-85870400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr4:85868800-85870400	Enhancers	Ovary	ovary
37	chr4:85869200-85869800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:85869200-85869800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:85869200-85869800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:85869200-85869800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:85869200-85869800	Enhancers	HSMMtube	muscle
42	chr4:85869200-85870000	Enhancers	NHDF-Ad	bronchial
43	chr4:85869200-85870200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:85869200-85870200	Enhancers	Brain Anterior Caudate	brain
45	chr4:85869200-85870200	Enhancers	Colon Smooth Muscle	Colon
46	chr4:85869200-85870400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:85869200-85870400	Enhancers	Adipose Nuclei	Adipose
48	chr4:85869200-85870400	Enhancers	Brain Angular Gyrus	brain
49	chr4:85869200-85870400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:85869200-85870400	Enhancers	Skeletal Muscle Female	skeletal muscle

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