Variant report

Variant	rs9991613
Chromosome Location	chr4:681940-681941
allele	C/T
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	chr4:681886-683772	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr4:680811-682027	K562	blood:	n/a	n/a
3	BHLHE40	chr4:680908-682002	K562	blood:	n/a	n/a
4	E2F6	chr4:681854-683709	H1-hESC	embryonic stem cell:	n/a	chr4:682298-682305 chr4:682298-682305 chr4:682294-682306 chr4:682669-682678 chr4:682298-682305
5	POLR2A	chr4:680627-682067	K562	blood:	n/a	n/a
6	POLR2A	chr4:681810-681985	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:680835-682128	HepG2	liver:	n/a	n/a
8	MAX	chr4:680764-682054	A549	lung:	n/a	n/a
9	ESR1	chr4:681516-681948	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:681802-682035	HCT-116	colon:	n/a	n/a
11	SMARCC1	chr4:680684-681985	Hela-S3	cervix:	n/a	chr4:681410-681419
12	HMGN3	chr4:680560-682198	K562	blood:	n/a	chr4:681195-681204
13	POLR2A	chr4:680810-682554	K562	blood:	n/a	n/a
14	SMARCB1	chr4:680524-682054	Hela-S3	cervix:	n/a	chr4:681410-681419

No.	Distal block	Cell Line	Cell type
1	chr4:680186..682717-chr4:773971..775707,2	MCF-7	breast:
2	chr4:681383..683193-chr4:698223..700658,3	K562	blood:
3	chr4:665676..669905-chr4:679525..682855,5	K562	blood:
4	chr4:680242..683670-chr4:697022..701034,8	MCF-7	breast:
5	chr4:680689..682702-chr4:985061..987897,2	K562	blood:
6	chr4:669988..672792-chr4:681146..683044,2	K562	blood:
7	chr4:681693..683683-chr4:698278..699853,2	K562	blood:

Variant related genes	Relation type
MFSD7	TF binding region
ENSG00000127415	Chromatin interaction
ENSG00000145217	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000169020	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10027549	1.00[ASN][1000 genomes]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs28470912	0.84[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	0.92[CEU][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs28630797	1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs3864130	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs4463020	0.84[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs4518182	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	1.00[ASN][1000 genomes]
rs71602496	1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	0.84[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs9992641	1.00[ASN][1000 genomes]
rs9998786	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
8	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
13	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
17	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv10413	chr4:667204-684301	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv593208	chr4:668000-682233	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv878250	chr4:668567-683842	Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv878251	chr4:669857-683842	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv878252	chr4:669857-685993	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9991613	POLN	cis	parietal	SCAN
rs9991613	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs9991613	RP11-1191J2.2	cis	Thyroid	GTEx
rs9991613	RP11-1191J2.2	cis	lung	GTEx
rs9991613	ZNF721	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:675200-682200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:675200-682400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:675200-682600	Weak transcription	GM12878-XiMat	blood
4	chr4:675400-682400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:676000-682000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:677000-682400	Enhancers	Fetal Muscle Leg	muscle
7	chr4:677800-682400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:678000-682000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:678200-682400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:678400-682200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:678400-682200	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:678400-682400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:678400-682400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:678400-682600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:678600-682000	Enhancers	Fetal Muscle Trunk	muscle
16	chr4:678800-682200	Weak transcription	Fetal Lung	lung
17	chr4:679200-682400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:680200-682400	Enhancers	Placenta	Placenta
19	chr4:680200-682400	Enhancers	Stomach Mucosa	stomach
20	chr4:680400-682000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:680400-682000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:680400-682200	Enhancers	Liver	Liver
23	chr4:680400-682200	Enhancers	Esophagus	oesophagus
24	chr4:680400-682200	Enhancers	Left Ventricle	heart
25	chr4:680400-682800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:680400-683000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:680600-682000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:680600-682200	Enhancers	Lung	lung
29	chr4:680600-682400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:680600-682400	Enhancers	Fetal Intestine Small	intestine
31	chr4:680600-682400	Enhancers	Psoas Muscle	Psoas
32	chr4:680600-682400	Enhancers	Right Atrium	heart
33	chr4:680600-682400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr4:680600-682400	Enhancers	Spleen	Spleen
35	chr4:680600-682400	Flanking Active TSS	HepG2	liver
36	chr4:680600-682600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:680600-682600	Enhancers	NH-A	brain
38	chr4:680600-682800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr4:680600-683600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr4:680600-684000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:680800-682000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:680800-682000	Enhancers	HMEC	breast
43	chr4:680800-682000	Flanking Active TSS	HSMMtube	muscle
44	chr4:680800-682200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr4:680800-682200	Flanking Active TSS	HSMM	muscle
46	chr4:680800-682200	Flanking Active TSS	K562	blood
47	chr4:680800-682400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:680800-682400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:680800-682400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:680800-682400	Flanking Active TSS	Colonic Mucosa	Colon

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