Variant report

Variant	rs7661609
Chromosome Location	chr4:85882849-85882850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85876909..85884375-chr4:85886007..85890757,11	MCF-7	breast:
2	chr4:85840711..85842530-chr4:85882246..85885030,2	MCF-7	breast:
3	chr4:85648671..85650306-chr4:85882299..85884684,2	MCF-7	breast:
4	chr4:85877992..85883015-chr4:85885939..85888953,5	MCF-7	breast:
5	chr4:85881229..85883388-chr4:85885235..85887298,2	K562	blood:

Variant related genes	Relation type
ENSG00000180769	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10029496	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856851	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856852	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11097028	0.82[EUR][1000 genomes]
rs11730981	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732309	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11732347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12498637	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498787	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12502559	0.81[EUR][1000 genomes]
rs12503215	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506456	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510410	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12640378	0.87[EUR][1000 genomes]
rs12648852	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13109918	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114115	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs13124246	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13125323	0.82[EUR][1000 genomes]
rs13139541	0.81[EUR][1000 genomes]
rs13141322	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13148035	0.89[EUR][1000 genomes]
rs1484660	0.85[AMR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs17009317	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs17009341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2046402	0.86[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869216	0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes]
rs28754901	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34239067	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34314581	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4131745	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4376130	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4464556	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470615	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4533765	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4624645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4626191	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4634212	0.86[EUR][1000 genomes]
rs55871210	0.82[EUR][1000 genomes]
rs56194765	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58074983	0.83[EUR][1000 genomes]
rs6531777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs67045782	0.88[AMR][1000 genomes]
rs67624868	0.82[EUR][1000 genomes]
rs6815917	0.81[EUR][1000 genomes]
rs6820517	0.82[EUR][1000 genomes]
rs6833661	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6835046	0.81[AMR][1000 genomes]
rs6847067	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857555	0.87[AMR][1000 genomes]
rs6858666	0.88[ASW][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.80[YRI][hapmap]
rs71597394	0.81[EUR][1000 genomes]
rs72664934	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72664952	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7654035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7675324	0.88[EUR][1000 genomes]
rs7682896	0.81[EUR][1000 genomes]
rs7692223	0.86[JPT][hapmap]
rs7694949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs7699226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684737	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9790649	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv879516	chr4:85877561-85895436	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7661609	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
4	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:85872000-85886600	Weak transcription	Lung	lung
6	chr4:85873400-85886600	Weak transcription	Esophagus	oesophagus
7	chr4:85873800-85884800	Weak transcription	HSMM	muscle
8	chr4:85873800-85885400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:85873800-85885800	Weak transcription	Osteobl	bone
10	chr4:85874000-85884600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:85874600-85886200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:85876400-85885400	Weak transcription	Left Ventricle	heart
13	chr4:85876600-85884200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:85876600-85885200	Weak transcription	Fetal Brain Male	brain
15	chr4:85877000-85885200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr4:85877400-85886200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:85877600-85883200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:85877600-85883200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:85877600-85885200	Weak transcription	Right Atrium	heart
20	chr4:85877600-85885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:85877600-85885400	Weak transcription	Brain Germinal Matrix	brain
22	chr4:85877600-85885400	Weak transcription	Placenta	Placenta
23	chr4:85877600-85885600	Weak transcription	NHEK	skin
24	chr4:85877600-85885800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:85877600-85886000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:85879600-85885200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:85879600-85886200	Weak transcription	Fetal Lung	lung
28	chr4:85879800-85885400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:85879800-85885400	Weak transcription	Aorta	Aorta
30	chr4:85879800-85885800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:85879800-85886200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:85880000-85883200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:85880000-85883200	Weak transcription	NHDF-Ad	bronchial
34	chr4:85880000-85884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:85880000-85884200	Weak transcription	Ovary	ovary
36	chr4:85880000-85885200	Weak transcription	Adipose Nuclei	Adipose
37	chr4:85880000-85885200	Weak transcription	HepG2	liver
38	chr4:85880000-85885400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:85880000-85885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:85880000-85885400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:85880000-85885400	Weak transcription	Fetal Intestine Large	intestine
42	chr4:85880000-85885400	Weak transcription	Gastric	stomach
43	chr4:85880000-85885400	Weak transcription	Pancreas	Pancrea
44	chr4:85880000-85885800	Weak transcription	Fetal Stomach	stomach
45	chr4:85880000-85886000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:85880000-85886200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:85880000-85886200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:85880000-85886200	Weak transcription	NH-A	brain
49	chr4:85880000-85886600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:85880000-85886600	Weak transcription	Spleen	Spleen

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