Variant report

Variant	rs2254580
Chromosome Location	chr1:179261761-179261762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:146)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:146 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:179261452-179261871	HepG2	liver:	n/a	chr1:179261621-179261633
2	ZC3H11A	chr1:179261591-179261820	K562	blood:	n/a	n/a
3	MYBL2	chr1:179261450-179261993	HepG2	liver:	n/a	n/a
4	RAD21	chr1:179261413-179261945	HepG2	liver:	n/a	chr1:179261621-179261633
5	RAD21	chr1:179261462-179261770	H1-hESC	embryonic stem cell:	n/a	chr1:179261621-179261633
6	RFX5	chr1:179261497-179261774	GM12878	blood:	n/a	chr1:179261675-179261692
7	CTCF	chr1:179261620-179261770	BJ	skin:	n/a	n/a
8	FOXA2	chr1:179261452-179262004	A549	lung:	n/a	n/a
9	MXI1	chr1:179261499-179261789	GM12878	blood:	n/a	n/a
10	HCFC1	chr1:179261504-179261845	K562	blood:	n/a	n/a
11	CTCF	chr1:179261467-179261853	K562	blood:	n/a	n/a
12	YY1	chr1:179261528-179261803	GM12878	blood:	n/a	n/a
13	RAD21	chr1:179261488-179261818	K562	blood:	n/a	chr1:179261621-179261633
14	CEBPB	chr1:179261533-179261965	Hela-S3	cervix:	n/a	n/a
15	ZKSCAN1	chr1:179261525-179261899	Hela-S3	cervix:	n/a	n/a
16	MAX	chr1:179261432-179261913	Hela-S3	cervix:	n/a	chr1:179261553-179261562
17	RCOR1	chr1:179261501-179261834	K562	blood:	n/a	n/a
18	MAX	chr1:179261569-179261821	GM12878	blood:	n/a	n/a
19	RAD21	chr1:179261462-179261988	A549	lung:	n/a	chr1:179261621-179261633
20	MAX	chr1:179261413-179261821	K562	blood:	n/a	chr1:179261553-179261562
21	MXI1	chr1:179261511-179261785	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr1:179261547-179261789	GM12878	blood:	n/a	n/a
23	CTCF	chr1:179261620-179261770	AG09309	skin:	n/a	n/a
24	JUND	chr1:179261514-179261853	K562	blood:	n/a	n/a
25	E2F4	chr1:179261693-179261852	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr1:179261539-179261796	MCF-7	breast:	n/a	n/a
27	CTCF	chr1:179261492-179261857	IMR90	lung:	n/a	n/a
28	CTCF	chr1:179261447-179261987	HCT-116	colon:	n/a	n/a
29	CTCF	chr1:179261620-179261770	HCM	heart:	n/a	n/a
30	RAD21	chr1:179261482-179261863	A549	lung:	n/a	chr1:179261621-179261633
31	CTCF	chr1:179261572-179261771	GM13977	blood:	n/a	n/a
32	SMC3	chr1:179261448-179261855	GM12878	blood:	n/a	n/a
33	EBF1	chr1:179261530-179261860	GM12878	blood:	n/a	n/a
34	FOS	chr1:179261505-179261912	MCF10A-Er-Src	breast:	n/a	n/a
35	RAD21	chr1:179261275-179262009	SK-N-SH	brain:	n/a	chr1:179261621-179261633
36	WRNIP1	chr1:179261482-179261841	GM12878	blood:	n/a	n/a
37	RAD21	chr1:179261553-179261832	GM12878	blood:	n/a	chr1:179261621-179261633
38	CTCF	chr1:179261489-179261865	K562	blood:	n/a	n/a
39	SP1	chr1:179261412-179261980	A549	lung:	n/a	chr1:179261494-179261504
40	CTCF	chr1:179261021-179262135	A549	lung:	n/a	n/a
41	CTCF	chr1:179261529-179261806	HepG2	liver:	n/a	n/a
42	RAD21	chr1:179261483-179261810	K562	blood:	n/a	chr1:179261621-179261633
43	CTCF	chr1:179261543-179261783	GM19238	blood:	n/a	n/a
44	CTCF	chr1:179261540-179261798	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr1:179261534-179261778	MCF-7	breast:	n/a	n/a
46	CTCF	chr1:179261536-179261792	GM19239	blood:	n/a	n/a
47	FOXA2	chr1:179261526-179261877	HepG2	liver:	n/a	n/a
48	CTCF	chr1:179261620-179261770	GM12867	blood:	n/a	n/a
49	CTCF	chr1:179261620-179261770	GM12866	blood:	n/a	n/a
50	BHLHE40	chr1:179261519-179261779	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179162970..179164096-chr1:179260953..179261863,4	MCF-7	breast:
2	chr1:179089527..179090473-chr1:179261292..179262134,2	K562	blood:
3	chr1:179220379..179221592-chr1:179260995..179261928,6	MCF-7	breast:
4	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
5	chr1:179260929..179262434-chr1:179560041..179562229,2	MCF-7	breast:
6	chr1:179220599..179221512-chr1:179261221..179261896,5	MCF-7	breast:
7	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
8	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
9	chr1:179261306..179262860-chr1:179282015..179283875,2	K562	blood:
10	chr1:179074423..179075428-chr1:179261348..179262132,3	MCF-7	breast:
11	chr1:179089981..179090796-chr1:179261194..179262105,4	MCF-7	breast:

No data

Variant related genes	Relation type
SOAT1	TF binding region
ENSG00000263633	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162782	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798655	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042899	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12138973	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12725375	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749666	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050451	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2152318	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2247061	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2248979	0.91[ASN][1000 genomes]
rs2250352	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2250477	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254214	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254623	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2255375	0.87[LWK][hapmap];0.87[YRI][hapmap]
rs2257089	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257100	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2484440	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2484443	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484446	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492777	0.91[ASN][1000 genomes]
rs2492778	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs2493116	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493117	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493118	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493119	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783391	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783392	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783393	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404818	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs433722	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652364	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56371666	0.91[ASN][1000 genomes]
rs61824366	0.89[ASN][1000 genomes]
rs6425530	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7523431	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.95[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2254580	TDRD5	cis	parietal	SCAN
rs2254580	RASAL2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179258400-179262400	Weak transcription	Fetal Kidney	kidney
2	chr1:179258600-179261800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:179258600-179261800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:179258600-179262000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:179258600-179262000	Weak transcription	Placenta	Placenta
6	chr1:179258600-179262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:179258600-179262200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:179258600-179262400	Weak transcription	Pancreas	Pancrea
9	chr1:179258600-179262400	Weak transcription	Stomach Mucosa	stomach
10	chr1:179258600-179262600	Weak transcription	Gastric	stomach
11	chr1:179258600-179262600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:179258800-179262200	Weak transcription	Fetal Intestine Large	intestine
13	chr1:179258800-179262400	Weak transcription	Colonic Mucosa	Colon
14	chr1:179260600-179261800	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:179260800-179262400	Enhancers	Brain Hippocampus Middle	brain
16	chr1:179261400-179261800	Enhancers	A549	lung
17	chr1:179261400-179261800	Enhancers	Hela-S3	cervix
18	chr1:179261400-179262000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:179261400-179262200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:179261400-179262200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:179261400-179262200	Enhancers	Liver	Liver
22	chr1:179261400-179262200	Enhancers	Brain Anterior Caudate	brain
23	chr1:179261400-179262200	Enhancers	Rectal Smooth Muscle	rectum
24	chr1:179261400-179262400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:179261400-179262400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:179261400-179262400	Enhancers	Brain Angular Gyrus	brain
27	chr1:179261400-179262400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:179261600-179261800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:179261600-179261800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:179261600-179262200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
31	chr1:179261600-179262200	Active TSS	Stomach Smooth Muscle	stomach
32	chr1:179261600-179262200	Flanking Active TSS	HepG2	liver
33	chr1:179261600-179262400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:179261600-179262400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:179261600-179262400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:179261600-179262400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:179261600-179262400	Enhancers	Brain Substantia Nigra	brain
38	chr1:179261600-179262400	Enhancers	Duodenum Smooth Muscle	Duodenum

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