Variant report

Variant	rs12059028
Chromosome Location	chr1:94316252-94316253
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr1:94316056-94316564	GM12878	blood:	n/a	n/a
2	REST	chr1:94316198-94316506	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr1:94316188-94316517	K562	blood:	n/a	n/a
4	CTCF	chr1:94316193-94316810	K562	blood:	n/a	n/a
5	RAD21	chr1:94316196-94316662	H1-hESC	embryonic stem cell:	n/a	n/a
6	CBX3	chr1:94316156-94316636	K562	blood:	n/a	n/a
7	SETDB1	chr1:94315987-94316632	U2OS	brain:	n/a	n/a
8	CTCF	chr1:94316244-94316618	A549	lung:	n/a	n/a
9	CTCF	chr1:94316180-94316470	K562	blood:	n/a	n/a
10	CBX3	chr1:94316163-94316539	K562	blood:	n/a	n/a
11	RAD21	chr1:94316219-94316607	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOSL2	chr1:94316211-94316613	HepG2	liver:	n/a	n/a
13	REST	chr1:94316097-94316532	PFSK-1	brain:	n/a	n/a
14	EBF1	chr1:94316180-94316520	GM12878	blood:	n/a	chr1:94316347-94316358
15	KAP1	chr1:94316183-94316435	U2OS	brain:	n/a	n/a
16	REST	chr1:94316224-94316460	Hela-S3	cervix:	n/a	n/a
17	TCF12	chr1:94316247-94316518	GM12878	blood:	n/a	n/a
18	RAD21	chr1:94316248-94316596	HepG2	liver:	n/a	n/a
19	REST	chr1:94316243-94316502	Hela-S3	cervix:	n/a	n/a
20	RUNX3	chr1:94316252-94316613	GM12878	blood:	n/a	n/a
21	RAD21	chr1:94316244-94316607	HepG2	liver:	n/a	n/a
22	CTCF	chr1:94316143-94316809	A549	lung:	n/a	n/a
23	KAP1	chr1:94316122-94316481	HEK293	kidney:	n/a	n/a
24	TCF3	chr1:94316235-94316514	GM12878	blood:	n/a	n/a
25	RAD21	chr1:94316236-94316600	SK-N-SH_RA	brain:	n/a	n/a
26	REST	chr1:94316139-94316579	PFSK-1	brain:	n/a	n/a
27	REST	chr1:94316238-94316503	K562	blood:	n/a	n/a
28	REST	chr1:94316169-94316606	PFSK-1	brain:	n/a	n/a
29	PAX5	chr1:94316056-94316631	GM12878	blood:	n/a	n/a
30	CBX3	chr1:94316203-94316558	HCT-116	colon:	n/a	n/a
31	PAX5	chr1:94316084-94316591	GM12878	blood:	n/a	n/a
32	EBF1	chr1:94316152-94316513	GM12878	blood:	n/a	chr1:94316347-94316358

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94311804..94314669-chr1:94314970..94317163,2	MCF-7	breast:
2	chr1:94315633..94319063-chr1:94342848..94345734,4	K562	blood:
3	chr1:94085637..94087323-chr1:94315969..94317684,2	MCF-7	breast:
4	chr1:94309833..94313487-chr1:94314841..94317688,5	K562	blood:
5	chr1:94307315..94310834-chr1:94315340..94316960,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FNBP1L-2	chr1:94312708-94317158	NONHSAT004550

No data

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000260464	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10874804	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10874805	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11165011	0.94[EUR][1000 genomes]
rs11165027	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11165028	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11165029	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11165032	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11805379	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808380	1.00[ASN][1000 genomes]
rs12062272	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062925	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069476	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076074	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078134	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080386	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12081399	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12090038	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12090230	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12094966	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17110374	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110608	1.00[ASN][1000 genomes]
rs2234729	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4075342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292667	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41292669	1.00[ASN][1000 genomes]
rs41292671	1.00[ASN][1000 genomes]
rs41292673	1.00[ASN][1000 genomes]
rs4542218	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57136451	1.00[ASN][1000 genomes]
rs58790885	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59444123	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59545065	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60057678	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61750895	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541397	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680755	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686765	1.00[ASN][1000 genomes]
rs6692306	1.00[ASN][1000 genomes]
rs6701957	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702045	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6702064	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6704348	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965451	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967332	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72969374	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7514067	1.00[ASN][1000 genomes]
rs7515991	1.00[ASN][1000 genomes]
rs7525516	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552401	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7555872	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
2	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314200-94317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:94314200-94332800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:94315600-94316800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:94316000-94316400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:94316000-94316400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:94316000-94316400	Enhancers	Brain Anterior Caudate	brain
9	chr1:94316000-94316400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
10	chr1:94316000-94316400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
11	chr1:94316000-94317200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:94316200-94316400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:94316200-94316400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:94316200-94316400	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr1:94316200-94316400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:94316200-94316400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:94316200-94316400	Enhancers	Adipose Nuclei	Adipose
18	chr1:94316200-94316400	Enhancers	Brain Hippocampus Middle	brain
19	chr1:94316200-94316400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:94316200-94316400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:94316200-94316400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:94316200-94316400	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:94316200-94316400	ZNF genes & repeats	Hela-S3	cervix
24	chr1:94316200-94316800	Enhancers	K562	blood

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