Variant report

Variant	rs4394721
Chromosome Location	chr1:212229471-212229472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:212228475-212229695	K562	blood:	n/a	n/a
2	SETDB1	chr1:212228617-212229546	K562	blood:	n/a	n/a
3	POLR2A	chr1:212228583-212229952	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:212228593-212229686	HL-60	blood:	n/a	n/a
5	POLR2A	chr1:212228973-212229848	K562	blood:	n/a	n/a
6	POLR2A	chr1:212228708-212229549	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:212229074-212229478	A549	lung:	n/a	n/a
8	SETDB1	chr1:212228409-212231670	K562	blood:	n/a	n/a
9	POLR2A	chr1:212228108-212230032	K562	blood:	n/a	n/a
10	POLR2A	chr1:212229458-212229476	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:212229100-212229531	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:212228631-212229747	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:212228603-212229771	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:212228599-212229732	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:212228212-212233601	K562	blood:	n/a	n/a
16	POLR2A	chr1:212228142-212230048	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212227506..212231237-chr1:212233553..212238482,7	K562	blood:
2	chr1:212223004..212226012-chr1:212226300..212230375,4	K562	blood:
3	chr1:212219058..212220568-chr1:212226723..212229507,2	K562	blood:
4	chr1:212208792..212210406-chr1:212229258..212230902,2	K562	blood:
5	chr1:212225925..212230498-chr1:212230640..212238482,9	K562	blood:

No data

Variant related genes	Relation type
RPL21P28	TF binding region
ENSG00000143476	Chromatin interaction
ENSG00000143493	Chromatin interaction
ENSG00000220749	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863936	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119843	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12066042	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12070369	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12076757	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089230	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1387814	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1387815	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17656163	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656362	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17656453	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17699790	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17700264	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2358333	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4093392	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951560	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4951561	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4951567	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55806741	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55960291	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56289586	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56292525	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828530	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828533	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828543	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61828547	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61830761	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675660	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66858610	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67417805	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519826	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525895	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7540968	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4394721	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212209600-212253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:212210800-212241200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:212215600-212233000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:212216200-212233200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:212217000-212232800	Strong transcription	Dnd41	blood
7	chr1:212218000-212231000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:212218000-212231800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:212225400-212230000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:212225800-212230000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:212226200-212233000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:212226200-212233000	ZNF genes & repeats	K562	blood
13	chr1:212226400-212230000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:212226600-212230400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:212226600-212237600	Weak transcription	NHDF-Ad	bronchial
16	chr1:212226800-212229800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:212227000-212230000	Strong transcription	HMEC	breast
18	chr1:212227000-212230600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:212227200-212230000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:212227200-212230000	Strong transcription	NHEK	skin
21	chr1:212227200-212230800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:212227200-212231200	Strong transcription	HepG2	liver
23	chr1:212227400-212229800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:212227400-212230000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:212227600-212230000	Strong transcription	Osteobl	bone
26	chr1:212227600-212230600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:212228200-212231200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr1:212228200-212231400	ZNF genes & repeats	GM12878-XiMat	blood
29	chr1:212228400-212229600	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr1:212228400-212229600	Strong transcription	NHLF	lung
31	chr1:212228400-212229800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:212228400-212229800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:212228400-212230000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr1:212228400-212230200	ZNF genes & repeats	A549	lung
35	chr1:212228600-212229600	Enhancers	Pancreas	Pancrea
36	chr1:212228600-212229800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:212228600-212229800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:212228600-212229800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212228600-212229800	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr1:212228600-212229800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:212228600-212230400	Strong transcription	HUVEC	blood vessel
42	chr1:212228600-212231600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr1:212228600-212231800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:212228600-212237800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:212228800-212229600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:212228800-212229600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:212228800-212229600	ZNF genes & repeats	Hela-S3	cervix
48	chr1:212228800-212229800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:212228800-212229800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:212228800-212230600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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