Variant report

Variant	rs11936545
Chromosome Location	chr4:88343187-88343188
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:88343136-88344193	GM12891	blood:	n/a	n/a
2	HCFC1	chr4:88342970-88344360	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:88343068-88343948	K562	blood:	n/a	n/a
4	POLR2A	chr4:88343005-88344214	IMR90	lung:	n/a	n/a
5	POLR2A	chr4:88341808-88344299	GM12878	blood:	n/a	n/a
6	FOXM1	chr4:88342587-88344359	GM12878	blood:	n/a	n/a
7	CHD1	chr4:88343151-88344297	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:88343065-88344204	GM12878	blood:	n/a	n/a
9	YY1	chr4:88343159-88343441	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:88342959-88344255	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:88342962-88344316	K562	blood:	n/a	n/a
12	NR2F2	chr4:88343106-88344322	K562	blood:	n/a	n/a
13	NFIC	chr4:88343086-88344244	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:88343123-88344267	GM18951	blood:	n/a	n/a
15	STAT5A	chr4:88343109-88344322	GM12878	blood:	n/a	chr4:88343136-88343144
16	MAX	chr4:88343155-88344295	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr4:88343153-88344199	HL-60	blood:	n/a	n/a
18	TRIM28	chr4:88343140-88344245	K562	blood:	n/a	n/a
19	POLR2A	chr4:88343128-88344212	K562	blood:	n/a	n/a
20	POLR2A	chr4:88343045-88344266	GM12892	blood:	n/a	n/a
21	MXI1	chr4:88343130-88344646	IMR90	lung:	n/a	n/a
22	MAX	chr4:88343147-88344319	K562	blood:	n/a	n/a
23	POLR2A	chr4:88342950-88344255	GM15510	blood:	n/a	n/a
24	BCLAF1	chr4:88343072-88344243	GM12878	blood:	n/a	n/a
25	RUNX3	chr4:88343050-88344246	GM12878	blood:	n/a	n/a
26	ELF1	chr4:88343127-88344264	GM12878	blood:	n/a	n/a
27	CTCF	chr4:88343080-88343230	GM12871	blood:	n/a	n/a
28	POLR2A	chr4:88343113-88344404	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr4:88343120-88343270	HCPEpiC	choroid plexus:	n/a	n/a
30	POLR2A	chr4:88343163-88344223	GM12878	blood:	n/a	n/a
31	TAF1	chr4:88343167-88344268	GM12878	blood:	n/a	n/a
32	MAX	chr4:88343155-88344310	A549	lung:	n/a	n/a
33	MTA3	chr4:88343012-88344245	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:88342816-88344247	K562	blood:	n/a	n/a
35	POLR2A	chr4:88342842-88344287	K562	blood:	n/a	n/a
36	POLR2A	chr4:88343099-88344258	GM19193	blood:	n/a	n/a
37	MAX	chr4:88343068-88344363	HepG2	liver:	n/a	n/a
38	POLR2A	chr4:88342052-88344383	GM12891	blood:	n/a	n/a
39	MYBL2	chr4:88343126-88344400	HepG2	liver:	n/a	n/a
40	CEBPB	chr4:88343151-88344174	GM12878	blood:	n/a	n/a
41	RUNX3	chr4:88343069-88344325	GM12878	blood:	n/a	n/a
42	MTA3	chr4:88342563-88344348	GM12878	blood:	n/a	n/a
43	JUN	chr4:88343059-88344491	K562	blood:	n/a	n/a
44	POLR2A	chr4:88343061-88344330	K562	blood:	n/a	n/a
45	RELA	chr4:88343161-88344279	GM15510	blood:	n/a	n/a
46	TAF1	chr4:88343100-88344262	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr4:88343067-88344329	HUVEC	blood vessel:	n/a	n/a
48	E2F6	chr4:88343138-88343279	K562	blood:	n/a	n/a
49	NRF1	chr4:88343046-88344019	SK-N-SH	brain:	n/a	chr4:88343646-88343660
50	MAX	chr4:88343078-88344307	K562	blood:	n/a	n/a

No data

(count:6 , 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	chr4:88341784..88343437-chr4:88384944..88387219,2	K562	blood:
4	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
5	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
6	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: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11936366	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11936844	1.00[YRI][hapmap]
rs56102037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56401941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59716710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60052062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6818444	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844206	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839721	0.96[AFR][1000 genomes]
rs73839773	1.00[AFR][1000 genomes];1.00[AMR][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88340800-88343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:88340800-88343200	Weak transcription	Gastric	stomach
3	chr4:88341400-88343400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:88341800-88343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:88341800-88343200	Weak transcription	Small Intestine	intestine
6	chr4:88342200-88343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:88342200-88343400	Flanking Active TSS	Liver	Liver
8	chr4:88342400-88343200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:88342400-88343200	Enhancers	Spleen	Spleen
10	chr4:88342400-88343200	Flanking Active TSS	Dnd41	blood
11	chr4:88342400-88344800	Active TSS	Brain Anterior Caudate	brain
12	chr4:88342400-88345400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:88342400-88345400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:88342600-88343200	Enhancers	Primary B cells from cord blood	blood
15	chr4:88342600-88343200	Weak transcription	Fetal Kidney	kidney
16	chr4:88342600-88343200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr4:88342600-88343200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr4:88342600-88343200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr4:88342600-88343400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:88342600-88343600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:88342600-88345000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:88342600-88345400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:88342600-88345400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr4:88342800-88343200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:88342800-88343200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:88342800-88343200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:88342800-88343200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:88342800-88343200	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr4:88342800-88343400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr4:88342800-88343400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr4:88342800-88343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:88342800-88343400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr4:88342800-88343400	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr4:88342800-88343400	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr4:88342800-88343400	Flanking Active TSS	HepG2	liver
37	chr4:88342800-88343600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:88342800-88343600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr4:88342800-88344800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr4:88342800-88344800	Active TSS	Brain Hippocampus Middle	brain
41	chr4:88342800-88345000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:88342800-88345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:88342800-88345000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:88342800-88345000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:88343000-88343200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr4:88343000-88343200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:88343000-88343200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr4:88343000-88343200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr4:88343000-88343200	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr4:88343000-88343200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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