Variant report

Variant	rs6688827
Chromosome Location	chr1:113945989-113945990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113943430..113947212-chr1:113950458..113953796,3	K562	blood:
2	chr1:113942426..113944033-chr1:113945413..113947084,2	MCF-7	breast:
3	chr1:113932882..113937661-chr1:113942406..113946072,7	MCF-7	breast:
4	chr1:113934736..113938053-chr1:113941345..113946073,4	K562	blood:
5	chr1:113941512..113944463-chr1:113944848..113948985,5	K562	blood:
6	chr1:113938477..113941904-chr1:113943268..113946445,5	MCF-7	breast:
7	chr1:113930552..113936083-chr1:113941902..113950756,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10458458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10458459	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs10857994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857996	0.81[EUR][1000 genomes]
rs11102627	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102628	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102636	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11102637	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11102638	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11102639	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs11102641	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11102647	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap]
rs1112085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1112543	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs12021783	0.99[ASN][1000 genomes]
rs12022213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12022849	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12023641	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs12024139	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12024428	0.97[ASN][1000 genomes]
rs12026682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12027235	0.83[EUR][1000 genomes]
rs12029305	0.93[ASN][1000 genomes]
rs12030900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs12032395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12034178	0.93[ASN][1000 genomes]
rs12038473	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12039669	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12039944	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12044485	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12045148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12045559	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12046451	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12049093	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12049447	0.81[CHB][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs12567622	0.93[ASN][1000 genomes]
rs12568854	0.92[ASN][1000 genomes]
rs1418607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1539411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs1573996	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs1936927	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1936928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2027536	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28661018	0.83[EUR][1000 genomes]
rs4838988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4839320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs4839323	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap]
rs4839324	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs55737954	0.99[ASN][1000 genomes]
rs72687924	0.93[ASN][1000 genomes]
rs9787276	0.97[ASN][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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS 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	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6688827	AFARP1	cis	cerebellum	SCAN
rs6688827	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113935200-113949400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:113935600-113949400	Weak transcription	Aorta	Aorta
3	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
4	chr1:113937200-113948200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:113937600-113947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:113937800-113946400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:113938000-113946200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:113939600-113947800	Weak transcription	HepG2	liver
10	chr1:113939800-113947200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:113939800-113947200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:113939800-113953400	Weak transcription	NHDF-Ad	bronchial
13	chr1:113940200-113948000	Weak transcription	Liver	Liver
14	chr1:113940200-113952200	Weak transcription	HMEC	breast
15	chr1:113940200-113987000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:113940800-113950000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:113940800-113952200	Weak transcription	Hela-S3	cervix
18	chr1:113941800-113952200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:113942000-113947200	Weak transcription	Fetal Heart	heart
20	chr1:113942200-113946200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:113942200-113947200	Weak transcription	Fetal Lung	lung
22	chr1:113942200-113947800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:113944200-113947800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:113944600-113948200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:113944600-113950600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:113944600-113958200	Weak transcription	Small Intestine	intestine
27	chr1:113944800-113950200	Weak transcription	A549	lung
28	chr1:113944800-113952200	Weak transcription	Stomach Mucosa	stomach
29	chr1:113945200-113946000	Enhancers	Gastric	stomach
30	chr1:113945200-113946000	Enhancers	Ovary	ovary
31	chr1:113945200-113946000	Enhancers	Pancreas	Pancrea
32	chr1:113945200-113946400	Enhancers	Left Ventricle	heart
33	chr1:113945200-113946800	Enhancers	Brain Germinal Matrix	brain
34	chr1:113945200-113948000	Enhancers	Right Atrium	heart
35	chr1:113945400-113946000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:113945400-113946000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:113945400-113946000	Enhancers	Esophagus	oesophagus
38	chr1:113945400-113946000	Enhancers	Lung	lung
39	chr1:113945600-113946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:113945600-113947000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:113945600-113948400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:113945800-113946000	Enhancers	Fetal Kidney	kidney
43	chr1:113945800-113946400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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