Variant report

Variant	rs4654625
Chromosome Location	chr1:228884158-228884159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228874211..228876992-chr1:228882867..228885336,2	K562	blood:
2	chr1:228877885..228881410-chr1:228882153..228885594,3	K562	blood:

Variant related genes	Relation type
ENSG00000116574	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006797	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10489542	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108502	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059178	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070785	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12075157	0.82[ASN][1000 genomes]
rs12076649	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077418	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12078927	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092986	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096381	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1535129	0.97[EUR][1000 genomes]
rs2009564	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2180162	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207704	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295255	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34036301	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806285	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3820265	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667385	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681268	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532644	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554565	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228873800-228884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:228873800-228884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:228875000-228884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:228876800-228884800	Weak transcription	Fetal Brain Male	brain
7	chr1:228877000-228884800	Weak transcription	Fetal Kidney	kidney
8	chr1:228877200-228889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228879200-228889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:228880400-228884200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:228880400-228885400	Weak transcription	A549	lung
12	chr1:228880400-228889400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:228880600-228889400	Weak transcription	Brain Anterior Caudate	brain
14	chr1:228880600-228889600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:228880600-228889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:228880600-228890400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:228881000-228884200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:228881000-228884800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:228881000-228886600	Weak transcription	Gastric	stomach
20	chr1:228881000-228886800	Weak transcription	HepG2	liver
21	chr1:228881000-228889200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:228881000-228889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:228881200-228884200	Weak transcription	Pancreas	Pancrea
24	chr1:228881200-228884400	Weak transcription	Small Intestine	intestine
25	chr1:228881200-228885200	Weak transcription	Brain Germinal Matrix	brain
26	chr1:228881200-228886200	Weak transcription	Primary T cells from cord blood	blood
27	chr1:228881200-228889600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:228881600-228889600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:228881800-228884200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:228882600-228887600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:228882800-228884200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:228882800-228884400	Enhancers	Placenta	Placenta
33	chr1:228882800-228889200	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:228882800-228889400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:228882800-228889400	Weak transcription	Brain Substantia Nigra	brain
36	chr1:228882800-228889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:228883000-228884800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:228883000-228884800	Weak transcription	Aorta	Aorta
39	chr1:228883000-228887800	Weak transcription	Spleen	Spleen
40	chr1:228883000-228889400	Weak transcription	Fetal Lung	lung
41	chr1:228883000-228889600	Weak transcription	Adipose Nuclei	Adipose
42	chr1:228883000-228889600	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:228883000-228893600	Weak transcription	Liver	Liver
44	chr1:228883200-228884800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:228883200-228885200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:228883200-228887400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:228883400-228887400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:228883400-228887400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:228883400-228887600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:228883400-228889200	Weak transcription	Brain Inferior Temporal Lobe	brain

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