Variant report

Variant	rs2789975
Chromosome Location	chr1:223116474-223116475
allele	G/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	POLR2A	chr1:223116411-223116514	Gliobla	brain:	n/a	n/a
2	POLR2A	chr1:223116436-223116513	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:223116457-223116492	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
NDUFB1P2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10495205	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17163557	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17163559	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17163564	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2609382	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609385	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609386	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609388	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609390	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609399	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2609400	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609403	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609405	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609406	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609407	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2789961	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2789966	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2789967	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35185132	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73128670	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1828950	chr1:223111708-223132433	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223102200-223119400	Weak transcription	NHLF	lung
2	chr1:223102200-223128000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:223102200-223130800	Weak transcription	Fetal Brain Male	brain
4	chr1:223102400-223121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:223102600-223117800	Weak transcription	Psoas Muscle	Psoas
6	chr1:223102600-223121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:223102800-223124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:223105000-223128800	Weak transcription	Ovary	ovary
9	chr1:223105200-223118400	Weak transcription	HSMMtube	muscle
10	chr1:223105400-223119000	Weak transcription	Right Atrium	heart
11	chr1:223108000-223120600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:223111600-223122800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:223112600-223126200	Weak transcription	Osteobl	bone
14	chr1:223113400-223119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:223114000-223118800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:223114000-223120000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:223114200-223118000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:223114200-223129000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:223114200-223130600	Weak transcription	Left Ventricle	heart
20	chr1:223114400-223117800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:223114600-223118400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:223114600-223122800	Weak transcription	Gastric	stomach
23	chr1:223114600-223124400	Weak transcription	Fetal Lung	lung
24	chr1:223114800-223121600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:223114800-223129200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:223115000-223118600	Weak transcription	Dnd41	blood
27	chr1:223115200-223117600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:223115200-223117600	Weak transcription	Thymus	Thymus
29	chr1:223115200-223117800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:223115200-223118000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:223115200-223118000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:223115200-223118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:223115200-223118800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:223115200-223119800	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:223115200-223121200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:223115200-223121800	Weak transcription	Fetal Kidney	kidney
37	chr1:223115200-223126600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:223115400-223117800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:223115400-223119000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:223116000-223116800	Strong transcription	Placenta	Placenta
41	chr1:223116000-223117000	Strong transcription	Primary T cells from cord blood	blood
42	chr1:223116200-223116600	Genic enhancers	Fetal Brain Female	brain
43	chr1:223116200-223116800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:223116200-223116800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:223116200-223116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:223116200-223116800	Strong transcription	Aorta	Aorta
47	chr1:223116200-223116800	Strong transcription	Liver	Liver
48	chr1:223116200-223116800	Strong transcription	Brain Substantia Nigra	brain
49	chr1:223116200-223116800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:223116200-223116800	Strong transcription	Fetal Intestine Small	intestine

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