Variant report

Variant	rs6537788
Chromosome Location	chr1:113931699-113931700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:113931155-113931707	HepG2	liver:	n/a	n/a
2	SETDB1	chr1:113930275-113931759	U2OS	brain:	n/a	n/a
3	SP1	chr1:113931101-113931775	A549	lung:	n/a	n/a
4	MYBL2	chr1:113931134-113931705	HepG2	liver:	n/a	n/a
5	KAP1	chr1:113930554-113933084	HEK293	kidney:	n/a	n/a
6	POLR2A	chr1:113931091-113931775	SK-N-SH	brain:	n/a	n/a
7	MYBL2	chr1:113931117-113931817	HepG2	liver:	n/a	n/a
8	MAX	chr1:113931107-113931793	A549	lung:	n/a	n/a
9	EP300	chr1:113931130-113931771	A549	lung:	n/a	n/a
10	FOXA2	chr1:113931108-113931804	A549	lung:	n/a	n/a
11	GATA1	chr1:113930839-113931840	PBDE	blood:	n/a	n/a
12	GATA3	chr1:113930714-113931911	SK-N-SH	brain:	n/a	n/a
13	SP1	chr1:113931156-113931879	A549	lung:	n/a	n/a
14	HDAC2	chr1:113931170-113931764	MCF-7	breast:	n/a	n/a
15	GATA2	chr1:113930773-113931818	SH-SY5Y	brain:	n/a	n/a
16	MXI1	chr1:113931258-113931711	HepG2	liver:	n/a	n/a
17	EP300	chr1:113931121-113931831	A549	lung:	n/a	n/a
18	MAX	chr1:113931045-113931817	MCF-7	breast:	n/a	n/a
19	EP300	chr1:113931183-113931721	SK-N-SH_RA	brain:	n/a	n/a
20	RAD21	chr1:113931070-113931761	SK-N-SH_RA	brain:	n/a	n/a
21	EP300	chr1:113930841-113931709	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr1:113931332-113931780	HepG2	liver:	n/a	n/a
23	NR2F2	chr1:113930853-113931864	MCF-7	breast:	n/a	n/a
24	RCOR1	chr1:113931103-113931796	K562	blood:	n/a	n/a
25	KAP1	chr1:113930717-113932926	U2OS	brain:	n/a	n/a
26	POLR2A	chr1:113931297-113933512	MCF-7	breast:	n/a	n/a
27	ZNF217	chr1:113930772-113931741	MCF-7	breast:	n/a	n/a
28	SIN3AK20	chr1:113931026-113931905	MCF-7	breast:	n/a	n/a
29	GATA3	chr1:113930757-113931738	T-47D	breast:	n/a	n/a
30	MAX	chr1:113931176-113931831	HepG2	liver:	n/a	n/a
31	GATA3	chr1:113930685-113931872	MCF-7	breast:	n/a	n/a
32	ARID3A	chr1:113931161-113931766	HepG2	liver:	n/a	n/a
33	NR2F2	chr1:113930993-113931850	MCF-7	breast:	n/a	n/a
34	TCF7L2	chr1:113931358-113931725	PANC-1	pancreas:	n/a	n/a
35	FOXA2	chr1:113930941-113932142	HepG2	liver:	n/a	n/a
36	TCF12	chr1:113931002-113931826	A549	lung:	n/a	n/a
37	SIN3A	chr1:113931674-113934672	H1-hESC	embryonic stem cell:	n/a	chr1:113933176-113933184 chr1:113933431-113933442
38	MXI1	chr1:113930460-113936450	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr1:113931441-113931717	ProgFib	skin:	n/a	n/a
40	TCF12	chr1:113930739-113931861	SK-N-SH	brain:	n/a	n/a
41	GATA3	chr1:113930854-113931979	MCF-7	breast:	n/a	n/a
42	RAD21	chr1:113931050-113931704	MCF-7	breast:	n/a	n/a
43	FOXA1	chr1:113931105-113931705	HepG2	liver:	n/a	n/a
44	FOXA1	chr1:113931108-113931743	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr1:113930653-113931978	MCF-7	breast:	n/a	n/a
46	TCF7L2	chr1:113930881-113931804	MCF-7	breast:	n/a	n/a
47	EP300	chr1:113930516-113935379	SK-N-SH	brain:	n/a	chr1:113935085-113935099
48	SP1	chr1:113931581-113932000	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113929860..113932778-chr17:56735135..56736789,2	MCF-7	breast:
2	chr1:113927002..113929717-chr1:113930255..113932026,2	MCF-7	breast:
3	chr1:113761704..113762671-chr1:113930964..113931744,2	MCF-7	breast:
4	chr1:113804322..113806527-chr1:113931501..113933105,2	MCF-7	breast:
5	chr1:113775818..113778014-chr1:113929925..113932483,2	MCF-7	breast:
6	chr1:113931119..113932828-chr1:113952487..113954122,2	K562	blood:
7	chr1:113820435..113822948-chr1:113930642..113932953,2	MCF-7	breast:
8	chr1:113822173..113823702-chr1:113930402..113933274,2	MCF-7	breast:
9	chr1:113930334..113933089-chr1:114124806..114127254,2	MCF-7	breast:
10	chr1:113751160..113752973-chr1:113930438..113931950,2	MCF-7	breast:
11	chr1:113930366..113932771-chr1:114217459..114219362,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAGI3	TF binding region
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11102629	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11102646	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs11578447	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs11579386	0.87[CEU][hapmap]
rs12117465	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119281	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125741	0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs12127683	0.96[EUR][1000 genomes]
rs12130729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs12130763	0.96[EUR][1000 genomes]
rs12131115	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs12134802	0.94[EUR][1000 genomes]
rs12135714	0.94[EUR][1000 genomes]
rs12144505	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145834	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17031376	1.00[ASN][1000 genomes]
rs17031640	0.87[CEU][hapmap]
rs17031645	0.87[CEU][hapmap]
rs17031648	0.87[CEU][hapmap]
rs17448063	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17461007	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17461231	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs1936931	0.96[EUR][1000 genomes]
rs2359415	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55710846	0.93[EUR][1000 genomes]
rs61817493	1.00[ASN][1000 genomes]
rs6671518	0.87[CEU][hapmap]
rs6696459	0.87[CEU][hapmap]
rs7514186	0.87[CEU][hapmap]
rs7528311	0.87[CEU][hapmap]
rs7533429	1.00[CEU][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs7555259	0.87[CEU][hapmap]

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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113931000-113931800	Enhancers	Fetal Kidney	kidney
2	chr1:113931000-113932000	Enhancers	K562	blood
3	chr1:113931200-113931800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:113931200-113931800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:113931200-113931800	Flanking Active TSS	Fetal Intestine Large	intestine
6	chr1:113931200-113931800	Enhancers	Placenta	Placenta
7	chr1:113931200-113931800	Flanking Active TSS	NHLF	lung
8	chr1:113931200-113932000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:113931200-113932000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:113931200-113932000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:113931200-113932000	Enhancers	Brain Angular Gyrus	brain
12	chr1:113931200-113932400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:113931200-113932400	Flanking Active TSS	HMEC	breast
14	chr1:113931200-113932400	Flanking Active TSS	NHEK	skin
15	chr1:113931200-113932600	Flanking Active TSS	Osteobl	bone
16	chr1:113931200-113934400	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:113931200-113935600	Active TSS	NHDF-Ad	bronchial
18	chr1:113931200-113937200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:113931400-113931800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:113931400-113931800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:113931400-113931800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:113931400-113931800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:113931400-113931800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:113931400-113931800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:113931400-113931800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:113931400-113931800	Enhancers	Adipose Nuclei	Adipose
27	chr1:113931400-113931800	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr1:113931400-113931800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:113931400-113931800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:113931400-113931800	Flanking Active TSS	NH-A	brain
31	chr1:113931400-113932000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr1:113931400-113932000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:113931400-113932000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:113931400-113932000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:113931400-113932000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:113931400-113932000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:113931400-113932000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:113931400-113932000	Enhancers	Brain Hippocampus Middle	brain
39	chr1:113931400-113932000	Enhancers	Brain Substantia Nigra	brain
40	chr1:113931400-113932000	Enhancers	Fetal Muscle Leg	muscle
41	chr1:113931400-113932000	Bivalent Enhancer	Fetal Thymus	thymus
42	chr1:113931400-113932200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:113931400-113932200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:113931400-113932200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:113931400-113932200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:113931400-113932400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:113931400-113932400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:113931400-113932400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:113931400-113932400	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:113931400-113932400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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