Variant report

Variant	rs259721
Chromosome Location	chr6:37791231-37791232
allele	C/G
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	MYC	chr6:37790840-37791427	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
2	MYC	chr6:37790779-37791562	MCF10A-Er-Src	breast:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
3	MXI1	chr6:37791212-37791393	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:37791117-37791444	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
5	MAX	chr6:37790791-37791528	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
6	GATA1	chr6:37790217-37791654	K562	blood:	n/a	chr6:37791124-37791131
7	TBL1XR1	chr6:37791231-37791337	K562	blood:	n/a	n/a
8	UBTF	chr6:37791171-37791347	K562	blood:	n/a	n/a
9	POLR2A	chr6:37790777-37791396	GM12878	blood:	n/a	n/a
10	MYC	chr6:37790725-37791416	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
11	MYC	chr6:37790718-37791554	MCF10A-Er-Src	breast:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
12	TEAD4	chr6:37791128-37791458	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZNF263	chr6:37790472-37791345	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:37790138..37792445-chr6:37803004..37804688,2	MCF-7	breast:
2	chr6:37788598..37791926-chr6:37799655..37801709,3	K562	blood:
3	chr6:37790878..37792753-chr6:37808430..37810032,2	K562	blood:
4	chr6:37788608..37792008-chr6:37826692..37829268,3	K562	blood:
5	chr6:37785884..37787754-chr6:37789028..37791294,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	TF binding region
ENSG00000225945	Chromatin interaction
ENSG00000243313	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11756656	0.83[ASN][1000 genomes]
rs1212636	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198360	0.92[ASN][1000 genomes]
rs12211975	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12523829	0.93[ASN][1000 genomes]
rs187741	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1979759	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2180514	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs259672	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259675	0.85[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs259676	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259678	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259683	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs259687	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs259688	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs259693	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs259714	0.87[ASN][1000 genomes]
rs259717	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs259722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259723	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3792706	0.82[JPT][hapmap]
rs4142102	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4711515	0.92[ASN][1000 genomes]
rs4711522	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4711523	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs6458030	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs67133782	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6912097	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915506	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6917668	1.00[YRI][hapmap]
rs6926280	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6934617	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6937655	0.93[ASN][1000 genomes]
rs72849334	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72849338	0.93[ASN][1000 genomes]
rs7765798	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9349051	0.93[ASN][1000 genomes]
rs9357255	0.86[CHD][hapmap]
rs9369024	0.83[ASN][1000 genomes]
rs9369025	0.82[ASN][1000 genomes]
rs9369029	0.85[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs9380703	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380704	0.93[ASN][1000 genomes]
rs9462374	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs9470714	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9470723	0.85[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9470724	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9470725	0.82[ASN][1000 genomes]
rs9647620	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs259721	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37788600-37791400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr6:37788600-37791400	Enhancers	Small Intestine	intestine
3	chr6:37788800-37791400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:37788800-37791400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:37788800-37791400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:37788800-37791400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:37788800-37791400	Enhancers	Brain Substantia Nigra	brain
8	chr6:37788800-37791400	Enhancers	Placenta	Placenta
9	chr6:37788800-37791400	Enhancers	Fetal Stomach	stomach
10	chr6:37788800-37791600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:37788800-37791800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:37788800-37792000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:37788800-37792000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:37789000-37791400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:37789000-37791400	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:37789000-37791400	Enhancers	Fetal Thymus	thymus
17	chr6:37789000-37791400	Enhancers	Ovary	ovary
18	chr6:37789000-37791400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:37789000-37791600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:37789000-37791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:37789000-37791600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:37789000-37791800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:37789000-37791800	Enhancers	Left Ventricle	heart
24	chr6:37789000-37791800	Enhancers	Lung	lung
25	chr6:37789000-37791800	Enhancers	Right Atrium	heart
26	chr6:37789000-37792200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:37789000-37794400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:37789000-37796400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:37789200-37791400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:37789200-37791400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:37789200-37791400	Enhancers	Gastric	stomach
32	chr6:37789200-37791400	Enhancers	Spleen	Spleen
33	chr6:37789200-37791600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:37789200-37791800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:37789400-37791400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:37789400-37791400	Enhancers	Brain Anterior Caudate	brain
37	chr6:37789400-37791400	Enhancers	Pancreas	Pancrea
38	chr6:37789400-37791800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:37789400-37792400	Enhancers	Fetal Brain Male	brain
40	chr6:37789400-37800000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:37789600-37791400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:37789600-37791400	Enhancers	Fetal Brain Female	brain
43	chr6:37789600-37791400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:37789600-37791600	Enhancers	Fetal Lung	lung
45	chr6:37789600-37792000	Enhancers	Fetal Muscle Trunk	muscle
46	chr6:37789800-37791600	Enhancers	Brain Germinal Matrix	brain
47	chr6:37790000-37791400	Enhancers	Psoas Muscle	Psoas
48	chr6:37790000-37791600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:37790200-37791400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr6:37790200-37791400	Flanking Active TSS	A549	lung

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