Variant report

Variant	rs597221
Chromosome Location	chr1:47131319-47131320
allele	A/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	chr1:47131284-47131981	GM12878	blood:	n/a	n/a
2	CTCF	chr1:47131280-47131430	RPTEC	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
2	chr1:47129860..47131954-chr1:47135983..47137506,2	K562	blood:

Variant related genes	Relation type
TEX38	TF binding region
ATPAF1	TF binding region
ENSG00000228237	Chromatin interaction
ENSG00000186118	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10890410	0.96[ASN][1000 genomes]
rs10890414	0.93[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	0.93[ASN][1000 genomes]
rs11211347	0.82[ASN][1000 genomes]
rs11801744	0.93[ASN][1000 genomes]
rs12562113	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12566278	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568734	0.93[ASN][1000 genomes]
rs1258055	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258058	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258063	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1258064	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258065	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258066	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258068	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258072	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1268714	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1273237	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13374909	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1745376	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933932	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146560	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241863	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241864	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439442	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476153	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476155	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476156	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476159	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486162	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3011290	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766218	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766220	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766221	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766222	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766223	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56771521	0.93[ASN][1000 genomes]
rs57495753	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583649	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58678760	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59479990	0.93[ASN][1000 genomes]
rs596794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604264	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631368	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631840	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636082	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636122	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636424	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648822	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655369	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657166	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs669647	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs673134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675731	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678466	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs683585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs689300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723333	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724309	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72900715	0.93[ASN][1000 genomes]
rs736188	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9094	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS 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	32 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	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
4	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
5	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
6	chr1:47109600-47132600	Weak transcription	HMEC	breast
7	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
9	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
10	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:47118000-47132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:47119000-47132400	Weak transcription	A549	lung
13	chr1:47119200-47132400	Weak transcription	Small Intestine	intestine
14	chr1:47121000-47133000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:47122400-47132000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:47122600-47132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:47122600-47133000	Weak transcription	Gastric	stomach
18	chr1:47122800-47132000	Weak transcription	NHLF	lung
19	chr1:47122800-47132200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:47123600-47131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:47123600-47132600	Weak transcription	HUVEC	blood vessel
22	chr1:47123600-47133000	Weak transcription	HSMMtube	muscle
23	chr1:47125200-47133000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:47125400-47131600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:47125400-47132000	Weak transcription	Fetal Brain Male	brain
26	chr1:47125400-47133000	Weak transcription	NH-A	brain
27	chr1:47126400-47132000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:47127000-47132200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:47127400-47131800	Strong transcription	Fetal Stomach	stomach
30	chr1:47127400-47132200	Weak transcription	Fetal Lung	lung
31	chr1:47128600-47131400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:47129200-47131400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:47129200-47131600	Strong transcription	Fetal Thymus	thymus
34	chr1:47129200-47132200	Strong transcription	Fetal Intestine Large	intestine
35	chr1:47129200-47132200	Strong transcription	Fetal Intestine Small	intestine
36	chr1:47129400-47131400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:47129400-47131400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:47129400-47131600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:47129400-47131600	Strong transcription	GM12878-XiMat	blood
40	chr1:47129400-47131600	Strong transcription	Osteobl	bone
41	chr1:47129400-47131800	Strong transcription	Primary B cells from cord blood	blood
42	chr1:47129400-47131800	Strong transcription	Placenta	Placenta
43	chr1:47129400-47131800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:47129400-47132000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:47129400-47132000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:47129400-47132000	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:47129400-47132200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:47129400-47132200	Strong transcription	Fetal Brain Female	brain
49	chr1:47129600-47131600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:47129800-47131600	Strong transcription	NHDF-Ad	bronchial

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