Variant report

Variant	rs11941041
Chromosome Location	chr4:20705838-20705839
allele	A/G
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	chr4:20705831-20705994	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20705332..20707768-chr4:20710083..20712545,3	K562	blood:
2	chr4:20702888..20705883-chr4:20707634..20710929,3	K562	blood:

Variant related genes	Relation type
PACRGL	TF binding region
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10011908	0.87[AMR][1000 genomes]
rs10017693	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10022322	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10024002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025286	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10034054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10084802	0.87[AFR][1000 genomes]
rs10805219	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10938801	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11944886	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12152652	0.85[EUR][1000 genomes]
rs12331966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641186	0.88[ASN][1000 genomes]
rs12644782	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12650007	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16869851	0.88[ASN][1000 genomes]
rs16869886	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16869889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985322	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2052775	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2114472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2114473	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2288308	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2322688	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28524474	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637181	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28714128	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28788006	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764965	0.86[ASN][1000 genomes]
rs3764966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764967	0.98[ASN][1000 genomes]
rs3796639	0.98[ASN][1000 genomes]
rs3815872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4414951	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4431223	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4510461	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640668	0.87[AFR][1000 genomes]
rs55794413	0.88[ASN][1000 genomes]
rs55874299	0.88[ASN][1000 genomes]
rs56152829	0.88[ASN][1000 genomes]
rs57740160	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59335491	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410099	0.88[ASN][1000 genomes]
rs62410126	0.98[ASN][1000 genomes]
rs62410129	0.94[ASN][1000 genomes]
rs62410159	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411662	0.91[ASN][1000 genomes]
rs6447974	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447975	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6447976	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447978	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6447982	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6811030	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6811505	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6815738	0.86[ASN][1000 genomes]
rs6817475	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6831295	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6831516	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73240292	0.98[ASN][1000 genomes]
rs7438098	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7655154	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660006	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7666288	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673805	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7674453	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681691	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7685481	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7696618	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs990206	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9995438	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20702600-20706000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:20702600-20706200	Weak transcription	Lung	lung
4	chr4:20702600-20717200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:20702800-20706000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:20702800-20706200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:20702800-20707400	Weak transcription	Aorta	Aorta
8	chr4:20703000-20706000	Weak transcription	Primary T cells from cord blood	blood
9	chr4:20703000-20706000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:20703000-20706000	Weak transcription	HSMMtube	muscle
11	chr4:20703000-20706200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:20703000-20706200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:20703000-20706200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:20703000-20706200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:20703000-20706200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:20703000-20706200	Weak transcription	Brain Substantia Nigra	brain
17	chr4:20703000-20706200	Weak transcription	Colonic Mucosa	Colon
18	chr4:20703000-20706200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:20703000-20706200	Weak transcription	Esophagus	oesophagus
20	chr4:20703000-20706200	Weak transcription	Fetal Kidney	kidney
21	chr4:20703000-20706200	Weak transcription	Placenta	Placenta
22	chr4:20703000-20706200	Weak transcription	Fetal Thymus	thymus
23	chr4:20703000-20706200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:20703000-20706200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:20703000-20706400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:20703000-20706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:20703000-20706400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:20703000-20706600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:20703000-20706600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:20703000-20707000	Weak transcription	Thymus	Thymus
31	chr4:20703000-20708600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:20703000-20717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
34	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
37	chr4:20703200-20706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:20703200-20706000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:20703200-20706200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:20703200-20706200	Weak transcription	Primary B cells from cord blood	blood
41	chr4:20703200-20706200	Weak transcription	Adipose Nuclei	Adipose
42	chr4:20703200-20706200	Weak transcription	Right Ventricle	heart
43	chr4:20703200-20706200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:20703200-20706200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr4:20703200-20706200	Weak transcription	NH-A	brain
46	chr4:20703200-20706400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:20703200-20706400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:20703200-20706400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr4:20703200-20706400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:20703200-20706600	Weak transcription	HSMM	muscle

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