Variant report

Variant	rs16850250
Chromosome Location	chr1:224804649-224804650
allele	A/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	MAX	chr1:224804544-224805111	H1-hESC	embryonic stem cell:	n/a	chr1:224805041-224805050
2	POLR2A	chr1:224803368-224805065	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr1:224804290-224804727	H1-neurons	neurons:	n/a	n/a
4	MAX	chr1:224804476-224805789	H1-hESC	embryonic stem cell:	n/a	chr1:224805041-224805050
5	POLR2A	chr1:224803273-224805067	U87	brain:	n/a	n/a
6	ZNF263	chr1:224803356-224805071	HEK293-T-REx	kidney:	n/a	chr1:224804289-224804298 chr1:224804498-224804507 chr1:224804351-224804360
7	MAX	chr1:224803269-224805331	H1-hESC	embryonic stem cell:	n/a	chr1:224803735-224803742 chr1:224805041-224805050
8	E2F6	chr1:224803256-224805378	H1-hESC	embryonic stem cell:	n/a	chr1:224803938-224803952 chr1:224803665-224803675 chr1:224804409-224804424 chr1:224805253-224805265
9	MXI1	chr1:224804519-224804986	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr1:224803117-224805791	H1-hESC	embryonic stem cell:	n/a	chr1:224803938-224803952 chr1:224803665-224803675 chr1:224804409-224804424 chr1:224805253-224805265
11	SUZ12	chr1:224804113-224806096	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTBP2	chr1:224803557-224806095	H1-hESC	embryonic stem cell:	n/a	n/a
13	SUZ12	chr1:224803428-224806408	NT2-D1	testis:	n/a	n/a
14	MAX	chr1:224804533-224805126	SK-N-SH	brain:	n/a	chr1:224805041-224805050

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224760255..224762194-chr1:224803067..224805853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233384	TF binding region
ENSG00000229991	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1004222	1.00[YRI][hapmap]
rs10495226	1.00[YRI][hapmap]
rs10915688	1.00[YRI][hapmap]
rs12117838	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs12124222	1.00[YRI][hapmap]
rs12125381	1.00[YRI][hapmap]
rs12130632	1.00[YRI][hapmap]
rs12131256	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs12135641	1.00[YRI][hapmap]
rs12136553	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs12137592	1.00[YRI][hapmap]
rs12139845	1.00[YRI][hapmap]
rs12143128	1.00[YRI][hapmap]
rs12143215	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs12143246	1.00[YRI][hapmap]
rs12564263	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1353837	0.91[ASN][1000 genomes]
rs16849875	0.91[EUR][1000 genomes]
rs16850015	0.94[EUR][1000 genomes]
rs16852083	1.00[YRI][hapmap]
rs16852090	1.00[YRI][hapmap]
rs2405527	1.00[YRI][hapmap]
rs41271539	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4654058	0.81[CHD][hapmap]
rs5002414	1.00[YRI][hapmap]
rs6658957	0.91[ASN][1000 genomes]
rs6666956	1.00[YRI][hapmap]
rs6672460	1.00[YRI][hapmap]
rs6699331	0.81[ASN][1000 genomes]
rs883115	0.81[CHD][hapmap]
rs904505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803200-224805800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr1:224803200-224805800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:224803200-224806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:224803200-224806400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
9	chr1:224803400-224804800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr1:224803400-224804800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:224803400-224805000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
12	chr1:224803400-224805000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:224803400-224805200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
14	chr1:224803400-224805200	Flanking Active TSS	Gastric	stomach
15	chr1:224803400-224805400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:224803400-224805800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:224803400-224805800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:224803400-224806800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
19	chr1:224803600-224804800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:224803600-224804800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:224803600-224804800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr1:224803600-224805000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:224803600-224805000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr1:224803600-224805000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
25	chr1:224803600-224805000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
26	chr1:224803600-224805000	Flanking Bivalent TSS/Enh	Right Ventricle	heart
27	chr1:224803600-224805000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
28	chr1:224803600-224805200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr1:224803600-224805200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr1:224803600-224805200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
31	chr1:224803600-224805400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:224803600-224805600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr1:224803600-224805800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:224803600-224805800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:224803600-224806200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr1:224803600-224806400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:224803800-224804800	Active TSS	Pancreas	Pancrea
38	chr1:224803800-224805000	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr1:224803800-224805000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
40	chr1:224803800-224805400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr1:224803800-224805400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:224803800-224805800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:224803800-224806200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:224803800-224806200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:224803800-224807800	Active TSS	NH-A	brain
46	chr1:224804000-224805000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
47	chr1:224804000-224805000	Flanking Bivalent TSS/Enh	Ovary	ovary
48	chr1:224804000-224805400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:224804200-224804800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:224804200-224804800	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood

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