Variant report

Variant	rs728130
Chromosome Location	chr11:77504996-77504997
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	chr11:77503943..77506099-chr11:77705414..77707567,2	MCF-7	breast:
2	chr11:77503485..77506288-chr11:77529799..77532684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149262	Chromatin interaction
ENSG00000087884	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11237260	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11237261	1.00[CHB][hapmap]
rs11237273	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11237300	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237342	1.00[CEU][hapmap]
rs11821643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11827910	1.00[YRI][hapmap]
rs12225695	1.00[CHB][hapmap]
rs12575416	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17825097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1790241	0.89[AMR][1000 genomes]
rs3018160	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7107540	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs7939005	0.85[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs728130	KCTD14	cis	cerebellum	SCAN
rs728130	OR2AT4	cis	parietal	SCAN
rs728130	NEU3	cis	parietal	SCAN
rs728130	RSF1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77463800-77527000	Weak transcription	Aorta	Aorta
2	chr11:77475200-77527800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:77475400-77522000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:77475400-77529000	Weak transcription	NHLF	lung
5	chr11:77475400-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:77475600-77511600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:77475600-77511600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:77475800-77510400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:77475800-77522000	Weak transcription	Hela-S3	cervix
10	chr11:77482600-77509800	Weak transcription	Adipose Nuclei	Adipose
11	chr11:77482800-77525800	Weak transcription	Fetal Lung	lung
12	chr11:77487400-77522000	Weak transcription	Placenta	Placenta
13	chr11:77489800-77511600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:77491400-77517600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr11:77495800-77528200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:77496000-77530200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:77497200-77506200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:77498800-77510200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:77499000-77525600	Weak transcription	HMEC	breast
20	chr11:77499200-77506000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:77499200-77511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:77499200-77513800	Weak transcription	NHEK	skin
23	chr11:77500000-77511400	Weak transcription	Fetal Heart	heart
24	chr11:77500200-77505800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:77500400-77505400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:77500400-77512200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:77500600-77505200	Weak transcription	Small Intestine	intestine
28	chr11:77500800-77505600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:77500800-77505600	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr11:77500800-77511600	Weak transcription	Brain Anterior Caudate	brain
31	chr11:77500800-77511600	Weak transcription	Psoas Muscle	Psoas
32	chr11:77501000-77506000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr11:77501200-77511400	Weak transcription	Spleen	Spleen
34	chr11:77501200-77525800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:77501400-77521600	Weak transcription	Fetal Kidney	kidney
36	chr11:77501400-77526800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:77501600-77511000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:77501800-77505000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:77501800-77505400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr11:77501800-77505400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:77502000-77516800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:77502200-77505000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:77502200-77511000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:77502400-77505000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr11:77502400-77505200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:77502400-77505200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr11:77502400-77515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:77502800-77505200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr11:77503000-77505000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:77503200-77505000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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