Variant report

Variant	rs3891250
Chromosome Location	chr4:658304-658305
allele	G/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	chr4:657857-658348	GM12891	blood:	n/a	n/a
2	ELF1	chr4:657736-658338	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:657234-658353	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr4:656777-658347	SK-N-SH	brain:	n/a	n/a
5	E2F6	chr4:657344-658305	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:657079-658351	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:657839-658361	GM12878	blood:	n/a	n/a
8	GABPA	chr4:657752-658418	MCF-7	breast:	n/a	chr4:658017-658026
9	GABPA	chr4:657279-658371	SK-N-SH	brain:	n/a	chr4:658017-658026
10	YY1	chr4:658142-658340	GM12878	blood:	n/a	n/a
11	E2F6	chr4:657230-658395	H1-hESC	embryonic stem cell:	n/a	n/a
12	PML	chr4:657750-658323	GM12878	blood:	n/a	n/a
13	ELF1	chr4:657030-658394	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:658187..662144-chr4:672176..676426,5	MCF-7	breast:
2	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272927	TF binding region
PDE6B	TF binding region
ENSG00000133256	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10027549	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10027866	0.94[ASW][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap]
rs10030136	1.00[ASN][1000 genomes]
rs10031745	0.81[ASW][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap]
rs1135375	1.00[ASN][1000 genomes]
rs13119162	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28374488	0.88[ASW][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs28407346	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28438498	0.88[MKK][hapmap]
rs28470912	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs28483373	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28488910	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28583078	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28586910	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28588872	0.81[AMR][1000 genomes]
rs28630797	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28675771	0.82[YRI][hapmap]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864130	1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs4463020	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs4505760	0.88[ASW][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71602496	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056602	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	1.00[CHD][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9985747	0.80[AMR][1000 genomes]
rs9991613	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs9992641	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3891250	ZNF721	cis	parietal	SCAN
rs3891250	POLN	cis	parietal	SCAN
rs3891250	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs3891250	RP11-1191J2.2	cis	lung	GTEx
rs3891250	RP11-1191J2.2	cis	Thyroid	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:656800-658400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr4:656800-658400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:656800-658400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:656800-658400	Active TSS	Fetal Intestine Large	intestine
5	chr4:656800-658800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:657000-658400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:657000-658400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:657000-658400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:657000-658400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:657000-658400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr4:657000-658400	Active TSS	Primary T cells from cord blood	blood
12	chr4:657000-658400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr4:657000-658400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:657000-658400	Flanking Active TSS	Fetal Brain Male	brain
15	chr4:657000-658400	Active TSS	Fetal Kidney	kidney
16	chr4:657000-658400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:657000-658400	Active TSS	Fetal Lung	lung
18	chr4:657000-658600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:657000-658600	Active TSS	GM12878-XiMat	blood
20	chr4:657200-658400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr4:657200-658400	Active TSS	Placenta Amnion	Placenta Amnion
22	chr4:657400-658400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:657400-658400	Active TSS	Rectal Smooth Muscle	rectum
24	chr4:657600-658400	Active TSS	Fetal Brain Female	brain
25	chr4:657600-658400	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr4:657800-658400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr4:657800-658400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr4:657800-658400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr4:657800-658400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr4:657800-658400	Flanking Active TSS	Fetal Thymus	thymus
31	chr4:657800-658400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr4:657800-658600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr4:657800-658600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:657800-658800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:657800-659000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:658000-658400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr4:658000-658400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr4:658000-658400	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr4:658000-658400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:658000-658400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr4:658000-658400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:658000-658400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr4:658000-658400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:658000-658400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr4:658000-658400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr4:658000-658400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:658000-658400	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr4:658000-658400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr4:658000-658400	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr4:658000-658400	Flanking Active TSS	Fetal Muscle Leg	muscle

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