Variant report

Variant	rs7823671
Chromosome Location	chr8:105600354-105600355
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr8:105599933-105602287	K562	blood:	n/a	chr8:105600627-105600637 chr8:105601356-105601365
2	POLR2A	chr8:105600267-105602170	K562	blood:	n/a	n/a
3	RCOR1	chr8:105600069-105601948	IMR90	lung:	n/a	n/a
4	RCOR1	chr8:105600292-105600613	GM12878	blood:	n/a	n/a
5	CHD1	chr8:105597872-105601900	GM12878	blood:	n/a	chr8:105601730-105601740
6	ARID3A	chr8:105599810-105600452	K562	blood:	n/a	n/a
7	TBL1XR1	chr8:105599620-105600603	K562	blood:	n/a	n/a
8	BHLHE40	chr8:105600254-105600630	K562	blood:	n/a	n/a
9	MXI1	chr8:105600345-105600600	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr8:105600272-105600648	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA2	chr8:105600106-105600619	SH-SY5Y	brain:	n/a	n/a
12	RUNX3	chr8:105600256-105600729	GM12878	blood:	n/a	n/a
13	RUNX3	chr8:105600095-105600718	GM12878	blood:	n/a	n/a
14	POLR2A	chr8:105596596-105602930	K562	blood:	n/a	n/a
15	POLR2A	chr8:105600106-105600518	GM12878	blood:	n/a	n/a
16	HMGN3	chr8:105600276-105602042	K562	blood:	n/a	n/a
17	WRNIP1	chr8:105600143-105600424	GM12878	blood:	n/a	n/a
18	EP300	chr8:105600205-105600405	GM12878	blood:	n/a	n/a
19	MAZ	chr8:105599837-105602298	IMR90	lung:	n/a	chr8:105600627-105600637 chr8:105601356-105601365
20	SIN3A	chr8:105600223-105602305	H1-hESC	embryonic stem cell:	n/a	chr8:105602050-105602063
21	MAX	chr8:105600341-105600540	GM12878	blood:	n/a	n/a
22	POLR2A	chr8:105600274-105602135	GM18951	blood:	n/a	n/a
23	POLR2A	chr8:105600315-105602882	K562	blood:	n/a	n/a
24	MYC	chr8:105600309-105600605	K562	blood:	n/a	n/a
25	JUND	chr8:105600283-105600595	K562	blood:	n/a	n/a
26	UBTF	chr8:105600006-105602351	K562	blood:	n/a	n/a
27	MAX	chr8:105600243-105602207	A549	lung:	n/a	chr8:105600627-105600637 chr8:105601356-105601365
28	CTBP2	chr8:105600348-105601777	H1-hESC	embryonic stem cell:	n/a	n/a
29	RCOR1	chr8:105599778-105602289	K562	blood:	n/a	n/a
30	POLR2A	chr8:105600064-105600636	GM12878	blood:	n/a	n/a
31	CEBPB	chr8:105600341-105600391	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr8:105597878-105602244	GM12878	blood:	n/a	n/a
33	MXI1	chr8:105599894-105602519	IMR90	lung:	n/a	n/a
34	MAX	chr8:105600215-105600667	K562	blood:	n/a	chr8:105600627-105600637
35	POLR2A	chr8:105600184-105601749	H1-hESC	embryonic stem cell:	n/a	n/a
36	MXI1	chr8:105598816-105602682	SK-N-SH	brain:	n/a	n/a
37	UBTF	chr8:105600234-105602105	K562	blood:	n/a	n/a
38	POLR2A	chr8:105600306-105600788	K562	blood:	n/a	n/a
39	MXI1	chr8:105600092-105600560	GM12878	blood:	n/a	n/a
40	POLR2A	chr8:105600122-105602817	K562	blood:	n/a	n/a
41	EP300	chr8:105600262-105600494	K562	blood:	n/a	n/a
42	POLR2A	chr8:105600205-105602669	GM12878	blood:	n/a	n/a
43	REST	chr8:105600082-105601906	H1-neurons	neurons:	n/a	chr8:105601642-105601652 chr8:105601694-105601703
44	RCOR1	chr8:105600303-105600571	K562	blood:	n/a	n/a
45	POLR2A	chr8:105600207-105600506	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:105599361..105601982-chr8:105602248..105604776,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253350	TF binding region
ENSG00000253350	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10505062	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10955352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955357	0.80[AMR][1000 genomes]
rs11775166	0.80[AMR][1000 genomes]
rs11776230	0.80[AMR][1000 genomes]
rs11777528	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11782865	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11782889	0.91[AFR][1000 genomes]
rs11783104	0.80[AMR][1000 genomes]
rs11783651	0.81[CEU][hapmap]
rs11784193	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11989936	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs11995774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11996303	0.89[AFR][1000 genomes]
rs12677524	1.00[JPT][hapmap]
rs12678904	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12678962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680250	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12681898	0.89[AFR][1000 genomes]
rs13249169	1.00[JPT][hapmap]
rs13250948	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs13264598	1.00[JPT][hapmap]
rs13265309	0.83[CEU][hapmap]
rs13266321	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266739	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs13268122	1.00[JPT][hapmap]
rs13268597	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13279448	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs16871500	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs16871634	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2028244	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28481880	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3018438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34008887	0.80[AMR][1000 genomes]
rs34255383	0.81[AFR][1000 genomes]
rs35263244	0.80[AMR][1000 genomes]
rs35328383	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35379160	0.80[AMR][1000 genomes]
rs35465370	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35467682	0.80[AMR][1000 genomes]
rs35649342	0.91[AFR][1000 genomes]
rs4236775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4263729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338071	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4593510	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4734803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59294667	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6468939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66494641	0.80[AMR][1000 genomes]
rs67089516	0.80[AMR][1000 genomes]
rs67712332	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990243	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6993149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6994764	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7004507	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap]
rs7010576	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71520892	0.82[AFR][1000 genomes]
rs7465442	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7815871	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7821181	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7834086	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs7841202	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7842204	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs7845137	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs9694676	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv508522	chr8:105532034-105614403	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2422460	chr8:105573376-105746329	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3369954	chr8:105600126-105602924	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7823671	LRP12	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105598600-105602400	Active TSS	GM12878-XiMat	blood
2	chr8:105598800-105600600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:105598800-105602000	Active TSS	Brain Anterior Caudate	brain
4	chr8:105598800-105602000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr8:105599000-105602000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:105599200-105602000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:105599200-105602400	Active TSS	Right Atrium	heart
8	chr8:105599200-105602400	Active TSS	Right Ventricle	heart
9	chr8:105599400-105600400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:105599400-105600600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:105599400-105600600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:105599400-105601000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr8:105599400-105602200	Active TSS	Left Ventricle	heart
14	chr8:105599600-105600400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr8:105599600-105600400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr8:105599600-105600400	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr8:105599600-105600400	Flanking Active TSS	Dnd41	blood
18	chr8:105599600-105600400	Flanking Active TSS	Osteobl	bone
19	chr8:105599600-105600600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr8:105599600-105600800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:105599600-105601800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr8:105599600-105602400	Active TSS	Colonic Mucosa	Colon
23	chr8:105599800-105600400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr8:105599800-105600400	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr8:105599800-105600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:105599800-105600600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr8:105599800-105601800	Active TSS	Fetal Brain Female	brain
28	chr8:105599800-105602000	Active TSS	Brain Angular Gyrus	brain
29	chr8:105599800-105602000	Active TSS	Brain Cingulate Gyrus	brain
30	chr8:105599800-105602200	Active TSS	Fetal Kidney	kidney
31	chr8:105599800-105602400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr8:105599800-105602400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr8:105599800-105602400	Active TSS	HSMMtube	muscle
34	chr8:105600000-105600400	Active TSS	Brain Germinal Matrix	brain
35	chr8:105600000-105600400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr8:105600000-105600400	Flanking Active TSS	Fetal Heart	heart
37	chr8:105600000-105600400	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr8:105600000-105600400	Flanking Active TSS	HUVEC	blood vessel
39	chr8:105600000-105600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr8:105600000-105600600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:105600000-105600600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr8:105600000-105600600	Flanking Active TSS	Hela-S3	cervix
43	chr8:105600000-105601200	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr8:105600000-105601400	Active TSS	Fetal Brain Male	brain
45	chr8:105600000-105601800	Active TSS	H1 Cell Line	embryonic stem cell
46	chr8:105600000-105601800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:105600000-105601800	Active TSS	Fetal Intestine Small	intestine
48	chr8:105600000-105601800	Active TSS	Fetal Muscle Trunk	muscle
49	chr8:105600000-105601800	Active TSS	K562	blood
50	chr8:105600000-105601800	Active TSS	NH-A	brain

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