Variant report

Variant	rs6833661
Chromosome Location	chr4:85839095-85839096
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	chr4:85834967..85837152-chr4:85837989..85839589,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10029496	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856851	0.91[AMR][1000 genomes];0.99[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];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11730981	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732309	0.85[EUR][1000 genomes]
rs11732347	0.85[EUR][1000 genomes]
rs12498637	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498787	0.84[EUR][1000 genomes]
rs12503215	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506456	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510410	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511112	0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs12640378	0.83[EUR][1000 genomes]
rs12648852	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109918	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114115	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs13124246	0.85[EUR][1000 genomes]
rs13141322	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13148035	0.84[EUR][1000 genomes]
rs1484660	0.84[AMR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs17009317	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs17009341	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046402	0.83[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869216	1.00[ASW][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs28754901	0.88[EUR][1000 genomes]
rs3098928	0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs34239067	0.83[EUR][1000 genomes]
rs34314581	0.86[EUR][1000 genomes]
rs4131745	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376130	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.88[TSI][hapmap]
rs4464556	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470615	0.82[EUR][1000 genomes]
rs4533765	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.88[TSI][hapmap]
rs4624645	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4626191	0.84[EUR][1000 genomes]
rs4634212	0.82[EUR][1000 genomes]
rs56194765	0.85[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];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.88[TSI][hapmap]
rs67045782	0.87[AMR][1000 genomes]
rs6835046	0.88[AMR][1000 genomes]
rs6847067	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857555	0.84[AMR][1000 genomes]
rs6858666	0.82[CHB][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs72664934	0.84[AMR][1000 genomes]
rs72664952	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664957	0.82[EUR][1000 genomes]
rs7654035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661609	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];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7675324	0.84[EUR][1000 genomes]
rs7685537	0.86[JPT][hapmap];0.95[MEX][hapmap]
rs7692223	0.86[JPT][hapmap]
rs7694949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9684737	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790649	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv879515	chr4:85789940-85843244	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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
rs6833661	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85781800-85848600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:85799600-85841600	Weak transcription	HMEC	breast
4	chr4:85801400-85843800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:85809000-85872800	Weak transcription	A549	lung
6	chr4:85811800-85851200	Weak transcription	Esophagus	oesophagus
7	chr4:85812800-85843600	Weak transcription	HepG2	liver
8	chr4:85813000-85858800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:85816000-85852400	Weak transcription	Left Ventricle	heart
10	chr4:85816800-85841600	Weak transcription	NH-A	brain
11	chr4:85821600-85858400	Weak transcription	Pancreas	Pancrea
12	chr4:85822600-85839800	Weak transcription	Fetal Brain Male	brain
13	chr4:85822600-85844800	Weak transcription	Placenta	Placenta
14	chr4:85825400-85840200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:85825400-85841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:85825400-85848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:85825400-85848600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:85825600-85848800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:85825600-85849000	Weak transcription	Fetal Intestine Large	intestine
20	chr4:85825600-85849000	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:85826200-85845400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:85826400-85849200	Weak transcription	Fetal Stomach	stomach
23	chr4:85827200-85848800	Weak transcription	Ovary	ovary
24	chr4:85829200-85850000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:85829200-85866200	Weak transcription	Spleen	Spleen
26	chr4:85834600-85845600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:85835000-85848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:85835200-85840200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:85835200-85841200	Weak transcription	NHEK	skin
30	chr4:85835200-85848400	Weak transcription	Fetal Lung	lung
31	chr4:85835400-85841600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:85835800-85839600	Enhancers	Brain Angular Gyrus	brain
33	chr4:85835800-85839800	Enhancers	Brain Hippocampus Middle	brain
34	chr4:85835800-85839800	Enhancers	Colon Smooth Muscle	Colon
35	chr4:85835800-85843600	Weak transcription	Fetal Intestine Small	intestine
36	chr4:85836000-85839800	Enhancers	Brain Substantia Nigra	brain
37	chr4:85836000-85839800	Enhancers	HUVEC	blood vessel
38	chr4:85836000-85840000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:85836200-85839200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:85836200-85839800	Enhancers	Osteobl	bone
41	chr4:85836400-85839800	Enhancers	NHDF-Ad	bronchial
42	chr4:85836600-85839400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:85836600-85839600	Enhancers	Brain Cingulate Gyrus	brain
44	chr4:85836800-85841600	Weak transcription	NHLF	lung
45	chr4:85837400-85839400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr4:85837400-85842400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:85837600-85840400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr4:85837600-85841400	Weak transcription	HSMMtube	muscle
49	chr4:85837600-85845600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:85837600-85858400	Weak transcription	Fetal Brain Female	brain

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