Variant report

Variant	rs4951662
Chromosome Location	chr1:213224297-213224298
allele	C/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	chr1:213224141-213225172	GM19099	blood:	n/a	n/a
2	POLR2A	chr1:213224233-213224912	A549	lung:	n/a	n/a
3	POLR2A	chr1:213224295-213224929	HepG2	liver:	n/a	n/a
4	USF1	chr1:213224253-213224650	A549	lung:	n/a	n/a
5	PML	chr1:213224160-213224679	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:213224296-213225054	GM15510	blood:	n/a	n/a
7	GABPA	chr1:213223988-213225290	HL-60	blood:	n/a	n/a
8	HCFC1	chr1:213224128-213225292	K562	blood:	n/a	n/a
9	POLR2A	chr1:213224243-213224743	GM12891	blood:	n/a	n/a
10	TCF12	chr1:213224238-213224771	A549	lung:	n/a	chr1:213224495-213224505
11	RUNX3	chr1:213224094-213225307	GM12878	blood:	n/a	n/a
12	MAX	chr1:213224174-213225213	K562	blood:	n/a	chr1:213224733-213224743 chr1:213225115-213225124
13	SMARCB1	chr1:213224268-213225150	Hela-S3	cervix:	n/a	chr1:213225114-213225123
14	MAX	chr1:213224069-213225224	K562	blood:	n/a	chr1:213224733-213224743 chr1:213225115-213225124
15	HEY1	chr1:213224177-213224853	HepG2	liver:	n/a	n/a
16	ETS1	chr1:213224080-213225170	K562	blood:	n/a	chr1:213224718-213224729 chr1:213224637-213224648 chr1:213224451-213224464
17	TBL1XR1	chr1:213224231-213225313	GM12878	blood:	n/a	n/a
18	CHD2	chr1:213224068-213225248	GM12878	blood:	n/a	chr1:213224140-213224147
19	SIN3AK20	chr1:213224287-213225038	PANC-1	pancreas:	n/a	n/a
20	MAX	chr1:213224297-213225440	NB4	blood:	n/a	chr1:213224733-213224743 chr1:213225115-213225124
21	ZMIZ1	chr1:213223456-213225344	K562	blood:	n/a	n/a
22	JUN	chr1:213224196-213225315	K562	blood:	n/a	chr1:213225115-213225123 chr1:213225114-213225124 chr1:213225115-213225122 chr1:213225114-213225124 chr1:213225114-213225124 chr1:213225114-213225124 chr1:213225115-213225123
23	E2F6	chr1:213224046-213224934	H1-hESC	embryonic stem cell:	n/a	chr1:213224685-213224695 chr1:213224721-213224731 chr1:213224140-213224147
24	YY1	chr1:213224182-213225139	K562	blood:	n/a	chr1:213224684-213224693 chr1:213224720-213224729 chr1:213224714-213224728 chr1:213224532-213224543 chr1:213224681-213224690
25	POLR2A	chr1:213224209-213224324	HUVEC	blood vessel:	n/a	n/a
26	NR2C2	chr1:213224207-213225083	Hela-S3	cervix:	n/a	chr1:213224582-213224591
27	POLR2A	chr1:213223867-213225263	K562	blood:	n/a	n/a
28	MAX	chr1:213224085-213224896	ECC-1	luminal epithelium:	n/a	chr1:213224733-213224743
29	ZNF263	chr1:213223733-213225272	HEK293-T-REx	kidney:	n/a	n/a
30	POLR2A	chr1:213223696-213225330	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:213224220-213225085	ProgFib	skin:	n/a	n/a
32	GATA1	chr1:213223891-213225401	PBDE	blood:	n/a	n/a
33	CHD2	chr1:213224168-213225286	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr1:213224047-213225281	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr1:213224243-213224765	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:213224153-213225267	SK-N-SH	brain:	n/a	n/a
37	ZBTB7A	chr1:213224226-213225058	K562	blood:	n/a	chr1:213224462-213224471
38	POLR2A	chr1:213224128-213225244	HUVEC	blood vessel:	n/a	n/a
39	HA-E2F1	chr1:213224187-213225209	MCF-7	breast:	n/a	chr1:213224685-213224695 chr1:213224721-213224731
40	MAX	chr1:213224197-213225060	GM12878	blood:	n/a	chr1:213224733-213224743
41	HEY1	chr1:213224158-213224781	K562	blood:	n/a	n/a
42	STAT5A	chr1:213224160-213225079	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:213224143-213225177	GM12892	blood:	n/a	n/a
44	YY1	chr1:213224248-213225137	GM12878	blood:	n/a	chr1:213224684-213224693 chr1:213224720-213224729 chr1:213224714-213224728 chr1:213224532-213224543 chr1:213224681-213224690
45	WRNIP1	chr1:213224018-213224619	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:213223998-213225335	PBDE	blood:	n/a	n/a
47	POLR2A	chr1:213224237-213224871	HepG2	liver:	n/a	n/a
48	CHD1	chr1:213224164-213225162	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:213224202-213224878	ECC-1	luminal epithelium:	n/a	n/a
50	ELF1	chr1:213224214-213224777	A549	lung:	n/a	chr1:213224730-213224742 chr1:213224584-213224593 chr1:213224721-213224733 chr1:213224720-213224729 chr1:213224583-213224594 chr1:213224681-213224690

No.	Distal block	Cell Line	Cell type
1	chr1:213187916..213191474-chr1:213223097..213226356,5	K562	blood:
2	chr1:213188825..213190728-chr1:213222994..213225299,2	MCF-7	breast:
3	chr1:213222798..213224539-chr1:213232214..213234723,3	K562	blood:
4	chr1:213187916..213189691-chr1:213222882..213226054,4	K562	blood:
5	chr1:213179534..213181909-chr1:213222762..213224304,2	K562	blood:
6	chr1:213184074..213185993-chr1:213223690..213226218,2	K562	blood:

Variant related genes	Relation type
RPS6KC1	TF binding region
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10465694	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10864034	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10864036	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11120082	0.80[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs1566247	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1566248	0.89[EUR][1000 genomes]
rs1976333	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2132428	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2172982	0.85[ASN][1000 genomes]
rs2494767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2817984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2935209	0.83[ASN][1000 genomes]
rs2935219	0.85[ASN][1000 genomes]
rs2936011	0.89[ASN][1000 genomes]
rs3002285	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs3010779	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs3010780	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs3010787	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs3010789	0.83[ASN][1000 genomes]
rs3124668	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs4543872	0.85[ASN][1000 genomes]
rs4951475	0.82[ASN][1000 genomes]
rs4951476	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951478	0.88[EUR][1000 genomes]
rs4951479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540774	0.90[EUR][1000 genomes]
rs6540776	0.89[EUR][1000 genomes]
rs6540778	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6540780	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540781	0.82[EUR][1000 genomes]
rs6657234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs6658259	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666814	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670025	0.87[ASN][1000 genomes]
rs6671872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs6679510	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6691488	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6692056	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6692144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697921	0.80[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs6699158	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4951662	RPS6KC1	cis	Artery Tibial	GTEx
rs4951662	ANGEL2	cis	parietal	SCAN
rs4951662	ANGEL2	cis	cerebellum	SCAN
rs4951662	BATF3	cis	parietal	SCAN
rs4951662	ANGEL2	cis	Nerve Tibial	GTEx
rs4951662	ANGEL2	cis	Esophagus Mucosa	GTEx
rs4951662	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213223600-213224400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr1:213223600-213224400	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr1:213223600-213224400	Flanking Active TSS	K562	blood
4	chr1:213223600-213225200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:213223600-213225200	Active TSS	Fetal Lung	lung
6	chr1:213223600-213225200	Active TSS	A549	lung
7	chr1:213223600-213225400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:213223600-213225800	Active TSS	Psoas Muscle	Psoas
9	chr1:213223600-213225800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:213223800-213224400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:213223800-213224400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr1:213223800-213224400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:213223800-213224400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr1:213223800-213224400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:213223800-213224400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:213223800-213224400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:213223800-213224400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:213223800-213224400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:213223800-213224600	Flanking Active TSS	Hela-S3	cervix
20	chr1:213223800-213224800	Active TSS	Primary B cells from cord blood	blood
21	chr1:213223800-213225200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:213223800-213225200	Active TSS	Fetal Kidney	kidney
23	chr1:213223800-213225200	Active TSS	NH-A	brain
24	chr1:213223800-213225400	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:213223800-213225600	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:213223800-213226000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:213224000-213224400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:213224000-213224400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:213224000-213224400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:213224000-213224400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:213224000-213224400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:213224000-213224400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:213224000-213224400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:213224000-213224400	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr1:213224000-213224400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr1:213224000-213224400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr1:213224000-213224400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:213224000-213224400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr1:213224000-213224400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:213224000-213224400	Flanking Active TSS	Liver	Liver
41	chr1:213224000-213224400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr1:213224000-213224400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr1:213224000-213224400	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr1:213224000-213224400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:213224000-213224400	Flanking Active TSS	Fetal Heart	heart
46	chr1:213224000-213224400	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr1:213224000-213224400	Flanking Active TSS	Stomach Mucosa	stomach
48	chr1:213224000-213224400	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr1:213224000-213224400	Flanking Active TSS	GM12878-XiMat	blood
50	chr1:213224000-213224400	Flanking Active TSS	HUVEC	blood vessel

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