Variant report

Variant	rs28609242
Chromosome Location	chr4:88342497-88342498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:88342245-88342669	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:88341808-88344299	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:88342319-88342616	K562	blood:	n/a	n/a
4	EP300	chr4:88342491-88342549	K562	blood:	n/a	n/a
5	POLR2A	chr4:88341803-88342727	K562	blood:	n/a	n/a
6	MAX	chr4:88342367-88342544	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:88341921-88342844	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:88342052-88344383	GM12891	blood:	n/a	n/a
9	POLR2A	chr4:88342303-88344277	GM18505	blood:	n/a	n/a
10	POLR2A	chr4:88342187-88344305	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:
2	chr4:88341987..88343662-chr4:88383872..88386006,2	MCF-7	breast:
3	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
4	chr4:88341784..88343437-chr4:88384944..88387219,2	K562	blood:
5	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
6	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
7	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD17B11-2	chr4:88341428-88343734	NONHSAT097311

No data

Variant related genes	Relation type
NUDT9	TF binding region
ENSG00000198189	Chromatin interaction
ENSG00000251716	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10010988	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10025902	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027786	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032597	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10035024	0.81[AMR][1000 genomes]
rs11945232	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103927	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13113575	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138404	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138636	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150578	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28372775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406846	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502849	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28701008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28736552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34549877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322242	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35371368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35607673	0.81[AMR][1000 genomes]
rs4314250	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816224	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854710	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7659182	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88334600-88342800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:88339400-88343000	Enhancers	Fetal Intestine Large	intestine
4	chr4:88340000-88343000	Enhancers	Fetal Intestine Small	intestine
5	chr4:88340000-88343000	Enhancers	Pancreas	Pancrea
6	chr4:88340400-88343000	Enhancers	Duodenum Mucosa	Duodenum
7	chr4:88340600-88342600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:88340600-88342600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:88340800-88342600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:88340800-88342600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:88340800-88342600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:88340800-88342600	Enhancers	Fetal Kidney	kidney
13	chr4:88340800-88342800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:88340800-88343000	Weak transcription	Colonic Mucosa	Colon
15	chr4:88340800-88343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:88340800-88343200	Weak transcription	Gastric	stomach
17	chr4:88341000-88343000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:88341200-88342800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:88341200-88343000	Weak transcription	Right Atrium	heart
20	chr4:88341400-88342800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:88341400-88343000	Weak transcription	HUVEC	blood vessel
22	chr4:88341400-88343400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:88341600-88342600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:88341600-88342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:88341600-88342800	Weak transcription	Psoas Muscle	Psoas
26	chr4:88341600-88343000	Weak transcription	NH-A	brain
27	chr4:88341800-88342800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:88341800-88343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:88341800-88343200	Weak transcription	Small Intestine	intestine
30	chr4:88342000-88342600	Enhancers	GM12878-XiMat	blood
31	chr4:88342000-88343000	Weak transcription	Stomach Mucosa	stomach
32	chr4:88342200-88343000	Weak transcription	A549	lung
33	chr4:88342200-88343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:88342200-88343400	Flanking Active TSS	Liver	Liver
35	chr4:88342400-88342600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:88342400-88342600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr4:88342400-88342600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:88342400-88342600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:88342400-88342600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:88342400-88342600	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:88342400-88342600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:88342400-88342800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr4:88342400-88342800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:88342400-88342800	Enhancers	Colon Smooth Muscle	Colon
45	chr4:88342400-88342800	Enhancers	HepG2	liver
46	chr4:88342400-88343000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:88342400-88343000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:88342400-88343000	Enhancers	Primary T cells from cord blood	blood
49	chr4:88342400-88343000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr4:88342400-88343000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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