Variant report

Variant	rs16835535
Chromosome Location	chr1:153723470-153723471
allele	C/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	RCOR1	chr1:153722856-153723526	K562	blood:	n/a	n/a
2	BHLHE40	chr1:153721885-153723522	K562	blood:	n/a	chr1:153722139-153722152
3	TAL1	chr1:153722833-153723522	K562	blood:	n/a	n/a
4	CCNT2	chr1:153723299-153723512	K562	blood:	n/a	n/a
5	GATA2	chr1:153722849-153723578	K562	blood:	n/a	chr1:153723035-153723044 chr1:153723337-153723346
6	TEAD4	chr1:153722789-153723554	K562	blood:	n/a	n/a
7	CTCF	chr1:153721665-153723546	A549	lung:	n/a	chr1:153722067-153722074 chr1:153722060-153722078 chr1:153722055-153722076 chr1:153722061-153722077
8	CUX1	chr1:153723284-153723551	K562	blood:	n/a	n/a
9	RCOR1	chr1:153722789-153723595	K562	blood:	n/a	n/a
10	STAT5A	chr1:153723107-153723500	K562	blood:	n/a	n/a
11	MAFK	chr1:153723277-153723551	K562	blood:	n/a	n/a
12	MAFF	chr1:153723265-153723559	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153720991..153724810-chr1:153725795..153729552,4	K562	blood:
2	chr1:153604905..153606814-chr1:153723152..153725405,2	K562	blood:
3	chr1:153720924..153726415-chr1:153745287..153750957,9	MCF-7	breast:
4	chr1:153721868..153723667-chr1:153746625..153749637,3	MCF-7	breast:
5	chr1:153698814..153704322-chr1:153719587..153724035,6	MCF-7	breast:
6	chr1:153721928..153724175-chr1:153731100..153734049,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GATAD2B-1	chr1:153723459-153723667	ENSG00000233222.2

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000143554	Chromatin interaction
ENSG00000238511	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs16835548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74115707	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription 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	48 gene(s)	inside rSNPs	diseases
2	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS 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	48 gene(s)	inside rSNPs	diseases
3	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
10	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
11	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
14	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
15	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers 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 target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
4	chr1:153712800-153725600	Strong transcription	Fetal Lung	lung
5	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
8	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
9	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
13	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:153713000-153725600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr1:153713000-153728600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
17	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:153713000-153747000	Strong transcription	Dnd41	blood
24	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:153715400-153724600	Strong transcription	NH-A	brain
27	chr1:153715400-153724800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:153715600-153725600	Strong transcription	NHEK	skin
30	chr1:153715600-153727600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
32	chr1:153715800-153724400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:153715800-153728400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:153718400-153727800	Strong transcription	Primary B cells from cord blood	blood
36	chr1:153718800-153724400	Strong transcription	NHLF	lung
37	chr1:153718800-153730000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:153719400-153725000	Strong transcription	Fetal Brain Male	brain
39	chr1:153719400-153727800	Strong transcription	HMEC	breast
40	chr1:153719400-153729000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:153719800-153731200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:153720000-153726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:153720200-153723800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:153721000-153726600	Weak transcription	Small Intestine	intestine
46	chr1:153721000-153738200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr1:153721400-153723600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:153721400-153723600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:153721400-153723600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:153721600-153724400	Enhancers	HUVEC	blood vessel

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