Variant report

Variant	rs28470912
Chromosome Location	chr4:665737-665738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:665400-665909	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:662898-665821	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:665218-665971	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:665236-665897	HL-60	blood:	n/a	n/a
5	POLR2A	chr4:665466-666047	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:664470-666409	K562	blood:	n/a	n/a
7	POLR2A	chr4:664333-665787	K562	blood:	n/a	n/a
8	POLR2A	chr4:664213-666126	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr4:664382-666059	Raji	blood:	n/a	n/a
10	POLR2A	chr4:665506-665942	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:665225-666085	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr4:665228-666005	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr4:665512-666118	H1-hESC	embryonic stem cell:	n/a	n/a
14	MTA3	chr4:665290-665760	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:665362-665869	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:664286-666056	GM12891	blood:	n/a	n/a
17	POLR2A	chr4:664212-666225	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:665234-665778	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:665220-666358	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:665385-665860	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr4:665525-666143	ECC-1	luminal epithelium:	n/a	n/a
22	HEY1	chr4:665365-666299	K562	blood:	n/a	n/a
23	POLR2A	chr4:665300-665929	GM12892	blood:	n/a	n/a
24	POLR2A	chr4:664315-666558	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:665354-665775	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:665232-666063	K562	blood:	n/a	n/a
27	POLR2A	chr4:665446-665870	HepG2	liver:	n/a	n/a
28	POLR2A	chr4:663370-666542	K562	blood:	n/a	n/a
29	POLR2A	chr4:665212-665756	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr4:664342-665772	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr4:663113-666359	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr4:665243-665877	GM12891	blood:	n/a	n/a
33	POLR2A	chr4:665544-666106	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:663210-666145	HepG2	liver:	n/a	n/a
35	POLR2A	chr4:663487-666318	K562	blood:	n/a	n/a
36	POLR2A	chr4:665667-665742	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr4:665328-665789	GM12891	blood:	n/a	n/a
38	POLR2A	chr4:665228-666099	GM12891	blood:	n/a	n/a
39	POLR2A	chr4:665169-666620	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:663475..665943-chr8:145718684..145721269,2	MCF-7	breast:
2	chr4:606087..607621-chr4:663295..666195,2	MCF-7	breast:
3	chr4:665676..669905-chr4:679525..682855,5	K562	blood:
4	chr4:663922..666504-chr4:705768..707927,2	MCF-7	breast:
5	chr4:664408..666949-chr4:770697..772344,2	MCF-7	breast:
6	chr4:640175..641727-chr4:663332..665885,2	K562	blood:
7	chr4:665710..668196-chr4:979815..981337,2	MCF-7	breast:
8	chr4:507198..510006-chr4:664346..666104,2	K562	blood:
9	chr4:665677..668201-chr4:979135..981223,2	K562	blood:

No data

Variant related genes	Relation type
MYL5	TF binding region
ENSG00000127415	Chromatin interaction
ENSG00000169026	Chromatin interaction
ENSG00000145214	Chromatin interaction
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10023472	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs10027549	1.00[ASN][1000 genomes]
rs10030136	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28525003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568555	1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28630797	1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs3864130	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs4463020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518182	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227539	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];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	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985747	0.81[EUR][1000 genomes]
rs9991613	0.84[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9992641	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
18	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28470912	RP11-1191J2.2	cis	lung	GTEx
rs28470912	RP11-1191J2.2	cis	Thyroid	GTEx
rs28470912	MFSD7	cis	Esophagus Muscularis	GTEx
rs28470912	POLN	cis	parietal	SCAN
rs28470912	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs28470912	ZNF721	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:658000-667000	Weak transcription	Small Intestine	intestine
2	chr4:658000-667400	Weak transcription	Aorta	Aorta
3	chr4:658200-666800	Weak transcription	Right Atrium	heart
4	chr4:658200-667000	Weak transcription	Stomach Mucosa	stomach
5	chr4:658200-667200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:658400-667000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:658600-667000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:658600-667000	Weak transcription	Fetal Brain Male	brain
9	chr4:659000-667000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:661200-666600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:662000-666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:663600-666000	Strong transcription	Dnd41	blood
13	chr4:663600-666400	Strong transcription	Brain Anterior Caudate	brain
14	chr4:663600-666600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:663600-667000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr4:663600-667000	Strong transcription	Brain Hippocampus Middle	brain
17	chr4:663600-667000	Strong transcription	Fetal Stomach	stomach
18	chr4:663600-667000	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:663800-666600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:663800-666600	Strong transcription	Fetal Intestine Small	intestine
21	chr4:663800-666800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:663800-666800	Strong transcription	Brain Germinal Matrix	brain
23	chr4:663800-666800	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr4:663800-666800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr4:663800-667000	Strong transcription	Primary T cells from cord blood	blood
26	chr4:663800-667000	Strong transcription	Brain Substantia Nigra	brain
27	chr4:664200-666200	Strong transcription	Brain Angular Gyrus	brain
28	chr4:664200-666600	Strong transcription	Fetal Muscle Leg	muscle
29	chr4:664200-666800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:664200-666800	Strong transcription	Thymus	Thymus
31	chr4:664200-667000	Strong transcription	Brain Cingulate Gyrus	brain
32	chr4:664400-666000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:664400-666200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:664400-666400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:664400-666400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:664400-666400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:664400-666400	Strong transcription	Esophagus	oesophagus
38	chr4:664400-666400	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr4:664400-666400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr4:664400-666600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:664400-666600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:664400-666600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:664400-666600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:664400-666600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:664400-666600	Strong transcription	Colon Smooth Muscle	Colon
46	chr4:664400-666600	Strong transcription	Left Ventricle	heart
47	chr4:664400-666800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:664400-666800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:664400-666800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:664400-666800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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