Variant report

Variant	rs3820265
Chromosome Location	chr1:228870417-228870418
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	CTCF	chr1:228870401-228871752	A549	lung:	n/a	chr1:228870813-228870831 chr1:228870816-228870829
2	RAD21	chr1:228870386-228872827	SK-N-SH	brain:	n/a	chr1:228870817-228870830
3	MXI1	chr1:228870038-228872688	SK-N-SH	brain:	n/a	n/a
4	REST	chr1:228870403-228872185	H1-neurons	neurons:	n/a	chr1:228870949-228870962
5	CTCF	chr1:228870362-228871645	SK-N-SH	brain:	n/a	chr1:228870813-228870831 chr1:228870816-228870829
6	MXI1	chr1:228870383-228872478	IMR90	lung:	n/a	n/a
7	GATA3	chr1:228870064-228870543	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
RHOU	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1006797	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12059178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12066510	1.00[CEU][hapmap]
rs12070785	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12075157	0.84[ASN][1000 genomes]
rs12076649	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077418	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12078927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096381	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535129	0.97[EUR][1000 genomes]
rs2009564	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2180162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34036301	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806285	0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4654625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654723	0.85[CEU][hapmap]
rs6665140	1.00[CEU][hapmap]
rs6667385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692721	0.85[CEU][hapmap]
rs7532644	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547333	1.00[CEU][hapmap]
rs7554565	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3405929	chr1:228869854-228872702	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228864000-228870600	Weak transcription	Placenta	Placenta
2	chr1:228868400-228870800	Weak transcription	Gastric	stomach
3	chr1:228869800-228871000	Enhancers	Fetal Brain Male	brain
4	chr1:228870200-228870600	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:228870200-228872000	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
7	chr1:228870400-228870600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:228870400-228870600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
9	chr1:228870400-228870600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:228870400-228870600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:228870400-228870600	Bivalent Enhancer	Primary B cells from cord blood	blood
12	chr1:228870400-228870600	Enhancers	Primary T cells from cord blood	blood
13	chr1:228870400-228870600	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:228870400-228870600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:228870400-228870600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:228870400-228870600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:228870400-228870600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:228870400-228870600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:228870400-228870600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:228870400-228870600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr1:228870400-228870600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:228870400-228870600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:228870400-228870600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:228870400-228870600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:228870400-228870600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:228870400-228870600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:228870400-228870600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:228870400-228870600	Active TSS	Adipose Nuclei	Adipose
29	chr1:228870400-228870600	Enhancers	Liver	Liver
30	chr1:228870400-228870600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:228870400-228870600	Enhancers	Brain Substantia Nigra	brain
32	chr1:228870400-228870600	Enhancers	Colon Smooth Muscle	Colon
33	chr1:228870400-228870600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:228870400-228870600	Bivalent Enhancer	Fetal Heart	heart
35	chr1:228870400-228870600	Flanking Active TSS	Fetal Kidney	kidney
36	chr1:228870400-228870600	Flanking Active TSS	Fetal Lung	lung
37	chr1:228870400-228870600	Active TSS	Fetal Muscle Trunk	muscle
38	chr1:228870400-228870600	Enhancers	Fetal Muscle Leg	muscle
39	chr1:228870400-228870600	Enhancers	Fetal Thymus	thymus
40	chr1:228870400-228870600	Weak transcription	Ovary	ovary
41	chr1:228870400-228870600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:228870400-228870600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:228870400-228870600	Flanking Active TSS	A549	lung
44	chr1:228870400-228870600	Enhancers	HepG2	liver
45	chr1:228870400-228870600	Bivalent Enhancer	NHEK	skin
46	chr1:228870400-228870800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:228870400-228870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:228870400-228870800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:228870400-228870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:228870400-228870800	Flanking Active TSS	Brain Germinal Matrix	brain

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