Variant report

Variant	rs940133
Chromosome Location	chr4:8473614-8473615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:8473409-8473619	K562	blood:	n/a	n/a
2	POLR2A	chr4:8473260-8473715	GM12878	blood:	n/a	n/a
3	HMGN3	chr4:8473515-8473691	K562	blood:	n/a	n/a
4	POLR2A	chr4:8473164-8473766	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:8473348-8473679	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:8470406-8476371	K562	blood:	n/a	n/a
7	POLR2A	chr4:8473416-8473651	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:8472717..8474725-chr4:8621251..8624026,2	K562	blood:
2	chr4:8472049..8473735-chr4:8474244..8476711,2	K562	blood:
3	chr4:8473000..8473785-chr4:8548526..8549174,2	MCF-7	breast:
4	chr4:8473110..8474734-chr4:8594190..8596233,2	MCF-7	breast:
5	chr4:8471024..8473735-chr4:8474244..8476611,2	K562	blood:

No data

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000155275	Chromatin interaction
ENSG00000109625	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10461079	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs1357481	0.97[EUR][1000 genomes]
rs1880023	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1880024	0.82[EUR][1000 genomes]
rs1916326	0.97[EUR][1000 genomes]
rs1949733	0.97[EUR][1000 genomes]
rs2140337	0.97[EUR][1000 genomes]
rs2255501	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386227	0.80[YRI][hapmap]
rs2450475	0.82[EUR][1000 genomes]
rs2631731	0.95[CEU][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes]
rs2631734	0.94[EUR][1000 genomes]
rs2631735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631736	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2631740	0.97[EUR][1000 genomes]
rs2631742	0.80[EUR][1000 genomes]
rs2631743	0.97[EUR][1000 genomes]
rs2631744	0.85[EUR][1000 genomes]
rs2631745	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[EUR][1000 genomes]
rs2631754	0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs2631758	0.97[EUR][1000 genomes]
rs2631768	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2688219	0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs2688223	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2688233	0.96[EUR][1000 genomes]
rs2688235	0.82[EUR][1000 genomes]
rs2688242	0.94[CEU][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes]
rs2688243	0.89[YRI][hapmap]
rs3103067	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3103069	0.95[EUR][1000 genomes]
rs3103070	0.83[EUR][1000 genomes]
rs3103071	0.97[EUR][1000 genomes]
rs3103072	0.96[EUR][1000 genomes]
rs3103099	0.94[EUR][1000 genomes]
rs4696828	0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs6447875	0.97[EUR][1000 genomes]
rs6837429	0.96[EUR][1000 genomes]
rs6845969	0.89[YRI][hapmap]
rs6858542	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs868105	0.97[EUR][1000 genomes]
rs871768	0.82[EUR][1000 genomes]
rs940134	0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs940136	0.89[YRI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs940133	RP11-689P11.2	cis	lung	GTEx
rs940133	TRMT44	cis	Nerve Tibial	GTEx
rs940133	ACOX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
2	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
3	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
4	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
9	chr4:8459400-8474000	Strong transcription	Fetal Intestine Small	intestine
10	chr4:8459800-8478800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:8463400-8473800	Weak transcription	Fetal Kidney	kidney
12	chr4:8463800-8478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:8464600-8474000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:8465200-8474000	Strong transcription	Lung	lung
15	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
16	chr4:8465400-8473800	Strong transcription	Fetal Intestine Large	intestine
17	chr4:8465400-8473800	Strong transcription	Pancreas	Pancrea
18	chr4:8465400-8473800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr4:8465400-8474200	Strong transcription	Gastric	stomach
20	chr4:8465400-8474200	Strong transcription	Spleen	Spleen
21	chr4:8465400-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:8465800-8474000	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:8465800-8474200	Strong transcription	Thymus	Thymus
24	chr4:8466600-8474200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:8466600-8474200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:8467600-8473800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:8467600-8475800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:8467600-8482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:8467800-8474200	Weak transcription	HSMM	muscle
30	chr4:8467800-8480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:8468000-8478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:8468400-8479600	Weak transcription	Psoas Muscle	Psoas
33	chr4:8470000-8474000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:8470000-8475400	Weak transcription	Small Intestine	intestine
35	chr4:8470600-8473800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:8470600-8473800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:8470600-8474000	Weak transcription	Stomach Mucosa	stomach
38	chr4:8470600-8479000	Weak transcription	Fetal Brain Male	brain
39	chr4:8471000-8473800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:8471200-8473800	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:8471200-8474000	Weak transcription	K562	blood
42	chr4:8471200-8475200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:8471200-8475200	Enhancers	Ovary	ovary
44	chr4:8471200-8476800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:8471200-8477400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:8471200-8480600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr4:8471400-8473800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:8471400-8473800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:8471400-8473800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:8471400-8473800	Weak transcription	NH-A	brain

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