Variant report

Variant	rs1235005
Chromosome Location	chr1:114417437-114417438
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:136)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:136 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:114417320-114417470	MCF-7	breast:	n/a	n/a
2	RAD21	chr1:114417254-114417451	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr1:114417246-114417489	K562	blood:	n/a	n/a
4	CTCF	chr1:114417317-114417460	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:114417290-114417471	Fibrobl	skin:	n/a	n/a
6	MAX	chr1:114417225-114417483	K562	blood:	n/a	chr1:114417431-114417442
7	CTCF	chr1:114417300-114417450	HCT-116	colon:	n/a	n/a
8	CTCF	chr1:114417320-114417470	AG04450	lung:	n/a	n/a
9	CTCF	chr1:114417300-114417450	GM12873	blood:	n/a	n/a
10	CTCF	chr1:114417172-114417549	GM12878	blood:	n/a	n/a
11	JUN	chr1:114416958-114417455	K562	blood:	n/a	n/a
12	BHLHE40	chr1:114416953-114417576	GM12878	blood:	n/a	n/a
13	MAX	chr1:114417315-114417529	H1-hESC	embryonic stem cell:	n/a	chr1:114417431-114417442
14	CTCF	chr1:114417280-114417463	GM10266	blood:	n/a	n/a
15	USF1	chr1:114417262-114417560	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr1:114417239-114417466	HepG2	liver:	n/a	n/a
17	CTCF	chr1:114417286-114417455	HepG2	liver:	n/a	n/a
18	CTCF	chr1:114417266-114417488	GM12878	blood:	n/a	n/a
19	CTCF	chr1:114417300-114417450	NB4	blood:	n/a	n/a
20	ZNF143	chr1:114417243-114417542	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr1:114417300-114417450	HPAF	blood vessel:	n/a	n/a
22	CTCF	chr1:114417320-114417470	HCT-116	colon:	n/a	n/a
23	CTCF	chr1:114417320-114417470	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr1:114417292-114417465	A549	lung:	n/a	n/a
25	MAX	chr1:114417205-114417515	GM12878	blood:	n/a	chr1:114417431-114417442
26	CTCF	chr1:114417300-114417450	GM12874	blood:	n/a	n/a
27	CTCF	chr1:114417309-114417460	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr1:114417264-114417496	Gliobla	brain:	n/a	n/a
29	CTCF	chr1:114417300-114417450	HEK293	kidney:	n/a	n/a
30	CTCF	chr1:114417300-114417450	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr1:114417300-114417450	AG09309	skin:	n/a	n/a
32	CTCF	chr1:114417300-114417450	GM12869	blood:	n/a	n/a
33	CTCF	chr1:114417300-114417450	GM12870	blood:	n/a	n/a
34	CTCF	chr1:114417300-114417450	GM12878	blood:	n/a	n/a
35	CTCF	chr1:114417249-114417501	MCF-7	breast:	n/a	n/a
36	JUND	chr1:114416935-114417543	K562	blood:	n/a	n/a
37	TEAD4	chr1:114416892-114417637	K562	blood:	n/a	n/a
38	CTCF	chr1:114417238-114417505	MCF-7	breast:	n/a	n/a
39	CTCF	chr1:114417296-114417476	MCF-7	breast:	n/a	n/a
40	CTCF	chr1:114417254-114417500	Hela-S3	cervix:	n/a	n/a
41	ATF1	chr1:114417055-114417477	K562	blood:	n/a	n/a
42	NFIC	chr1:114416530-114417590	GM12878	blood:	n/a	n/a
43	CTCF	chr1:114417300-114417450	A549	lung:	n/a	n/a
44	CTCF	chr1:114417360-114417510	RPTEC	kidney:	n/a	n/a
45	SMC3	chr1:114417057-114417484	GM12878	blood:	n/a	n/a
46	MYC	chr1:114417333-114417442	MCF-7	breast:	n/a	chr1:114417431-114417442
47	CTCF	chr1:114417320-114417470	HPF	lung:	n/a	n/a
48	CTCF	chr1:114417340-114417490	HA-sp	spinal cord:	n/a	n/a
49	CTCF	chr1:114417320-114417470	HCM	heart:	n/a	n/a
50	CTCF	chr1:114417300-114417450	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114396190..114400486-chr1:114415320..114417523,4	MCF-7	breast:
2	chr1:114416696..114418511-chr1:114445493..114447564,2	K562	blood:
3	chr1:114416299..114419266-chr1:114473123..114475526,3	MCF-7	breast:
4	chr1:114416727..114419302-chr20:56273752..56275590,2	MCF-7	breast:
5	chr1:114410354..114414312-chr1:114415133..114418521,4	K562	blood:
6	chr1:114415714..114417766-chr1:114443155..114445655,2	MCF-7	breast:
7	chr1:114415189..114417454-chr1:114422016..114424443,3	MCF-7	breast:
8	chr1:114414556..114418668-chr1:114471915..114474547,3	K562	blood:
9	chr1:114391365..114395021-chr1:114417111..114420542,3	MCF-7	breast:
10	chr1:114417177..114417796-chr1:114505802..114506345,2	MCF-7	breast:
11	chr1:114377679..114378960-chr1:114416919..114417937,6	MCF-7	breast:
12	chr1:114415510..114417903-chr1:114447530..114449794,2	MCF-7	breast:
13	chr1:114417201..114419873-chr1:114437424..114440357,2	MCF-7	breast:

No data

Variant related genes	Relation type
PTPN22	TF binding region
ENSG00000235527	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134242	Chromatin interaction
ENSG00000226167	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1111695	0.95[CHD][hapmap];0.97[GIH][hapmap]
rs1217378	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217379	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217404	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1217405	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1217406	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1217409	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217411	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217414	0.94[LWK][hapmap];0.87[YRI][hapmap]
rs1217418	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217419	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217420	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230682	0.80[ASN][1000 genomes]
rs1230686	0.80[ASN][1000 genomes]
rs1310182	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1539437	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2185971	0.95[CHD][hapmap];0.97[GIH][hapmap]
rs2273758	1.00[CHD][hapmap];0.97[GIH][hapmap]
rs2476600	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2476604	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2797414	1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[ASN][1000 genomes]
rs2797416	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789598	1.00[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs3789600	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4991898	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6537798	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6665194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672018	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7555634	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114410000-114417800	Enhancers	NHEK	skin
2	chr1:114412600-114417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:114414200-114417600	Enhancers	HUVEC	blood vessel
4	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:114415200-114418200	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:114415200-114418600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:114415400-114417600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:114415400-114417800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:114415400-114419000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:114415400-114428800	Weak transcription	Colonic Mucosa	Colon
11	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
12	chr1:114415600-114417600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr1:114415600-114417600	Enhancers	Primary T cells from cord blood	blood
14	chr1:114415600-114417800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:114415600-114417800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:114415600-114418000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:114415600-114418200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:114415600-114418400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:114415600-114418800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:114415800-114418200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:114415800-114418800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:114416000-114417800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:114416400-114417600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:114416600-114417600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:114416600-114417600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr1:114416600-114417600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:114416600-114417600	Enhancers	HMEC	breast
28	chr1:114416600-114417600	Enhancers	K562	blood
29	chr1:114416600-114417800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:114416600-114417800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:114417000-114423600	Weak transcription	Stomach Mucosa	stomach
32	chr1:114417200-114417600	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:114417200-114419000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:114417200-114419200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
36	chr1:114417400-114417800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:114417400-114418800	Enhancers	Small Intestine	intestine
38	chr1:114417400-114419000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr1:114417400-114419200	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:114417400-114421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:114417400-114421800	Weak transcription	Dnd41	blood

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