Variant report

Variant	rs61738616
Chromosome Location	chr1:173939729-173939730
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	CTCF	chr1:173939616-173939741	MCF-7	breast:	n/a	n/a
2	MAFK	chr1:173939416-173939753	IMR90	lung:	n/a	chr1:173939581-173939597 chr1:173939585-173939596 chr1:173939584-173939598
3	GATA3	chr1:173939637-173939743	SH-SY5Y	brain:	n/a	n/a
4	MAFK	chr1:173939426-173939732	HepG2	liver:	n/a	chr1:173939581-173939597 chr1:173939585-173939596 chr1:173939584-173939598
5	POLR2A	chr1:173939651-173939739	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:173939609-173939745	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173939340..173940107-chr1:174043783..174044572,3	MCF-7	breast:

Variant related genes	Relation type
RNA5SP68	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16846493	0.83[AMR][1000 genomes]
rs58700482	1.00[EUR][1000 genomes]
rs60317356	1.00[EUR][1000 genomes]
rs6425263	1.00[EUR][1000 genomes]
rs6425269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6667235	0.83[AMR][1000 genomes]
rs6671810	0.83[AMR][1000 genomes]
rs6677446	1.00[EUR][1000 genomes]
rs6678061	0.83[AMR][1000 genomes]
rs6686659	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551109	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7554635	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:173901600-173966400	Strong transcription	Dnd41	blood
12	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:173905200-173954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:173906000-173940400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:173906800-173959000	Strong transcription	Liver	Liver
21	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:173910400-173952200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
24	chr1:173922200-173942000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:173922200-173954000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:173923400-173954400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:173923600-173939800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr1:173923800-173953800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:173923800-173954400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:173923800-173955600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:173924000-173940200	Strong transcription	Osteobl	bone
33	chr1:173927600-173954200	Strong transcription	Placenta	Placenta
34	chr1:173928600-173940200	Strong transcription	Fetal Thymus	thymus
35	chr1:173928600-173942200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:173928800-173953800	Strong transcription	Fetal Intestine Large	intestine
37	chr1:173929000-173940000	Strong transcription	NHDF-Ad	bronchial
38	chr1:173929000-173962200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:173929600-173942600	Strong transcription	GM12878-XiMat	blood
40	chr1:173929600-173952800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:173930400-173941400	Weak transcription	Fetal Heart	heart
42	chr1:173931000-173940800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:173931000-173946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:173931200-173944000	Strong transcription	HUVEC	blood vessel
45	chr1:173931200-173946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:173931200-173949800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
50	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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