Variant report

Variant	rs2952522
Chromosome Location	chr7:25605515-25605516
allele	C/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	SMC3	chr7:25604902-25607116	SK-N-SH	brain:	n/a	chr7:25605656-25605670 chr7:25605700-25605714
2	CTCF	chr7:25605201-25606159	HepG2	liver:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
3	CTCF	chr7:25605218-25606150	HCT-116	colon:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
4	RAD21	chr7:25605247-25605910	SK-N-SH_RA	brain:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
5	CTCF	chr7:25605317-25606017	K562	blood:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
6	RAD21	chr7:25605336-25606028	HCT-116	colon:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
7	RFX5	chr7:25605197-25605704	K562	blood:	n/a	n/a
8	CTCF	chr7:25605254-25606051	K562	blood:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
9	RUNX3	chr7:25605455-25605911	GM12878	blood:	n/a	n/a
10	RFX5	chr7:25605506-25605852	Hela-S3	cervix:	n/a	n/a
11	YY1	chr7:25605469-25605833	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr7:25605419-25605919	H1-hESC	embryonic stem cell:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
13	GTF2F1	chr7:25605493-25605852	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr7:25605496-25605870	K562	blood:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
15	RAD21	chr7:25605400-25605936	ECC-1	luminal epithelium:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
16	CEBPB	chr7:25605426-25605977	A549	lung:	n/a	chr7:25605716-25605729
17	CTCF	chr7:25605087-25606278	HCT-116	colon:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
18	ZNF384	chr7:25605464-25605876	K562	blood:	n/a	n/a
19	RAD21	chr7:25605421-25605860	H1-hESC	embryonic stem cell:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
20	CTCF	chr7:25605507-25605875	HUVEC	blood vessel:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
21	RAD21	chr7:25605430-25605923	A549	lung:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
22	ZNF143	chr7:25605486-25605883	K562	blood:	n/a	n/a
23	ARID3A	chr7:25605491-25605914	HepG2	liver:	n/a	n/a
24	RAD21	chr7:25605471-25605830	GM12878	blood:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
25	RAD21	chr7:25605443-25605854	H1-hESC	embryonic stem cell:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
26	RAD21	chr7:25605416-25605983	MCF-7	breast:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
27	YY1	chr7:25605489-25605795	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr7:25605336-25605958	K562	blood:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
29	CTCF	chr7:25605412-25605931	ECC-1	luminal epithelium:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
30	CTCF	chr7:25605438-25605891	A549	lung:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
31	CTCF	chr7:25605295-25606053	MCF-7	breast:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
32	USF1	chr7:25605485-25605836	A549	lung:	n/a	n/a
33	CEBPB	chr7:25605503-25605884	A549	lung:	n/a	chr7:25605716-25605729
34	RAD21	chr7:25605435-25605912	Hela-S3	cervix:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
35	CTCF	chr7:25605406-25605981	ECC-1	luminal epithelium:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
36	CTCF	chr7:25605511-25605862	T-47D	breast:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
37	SMC3	chr7:25605348-25606103	GM12878	blood:	n/a	chr7:25605656-25605670 chr7:25605700-25605714
38	SMC3	chr7:25605480-25605902	Hela-S3	cervix:	n/a	chr7:25605656-25605670 chr7:25605700-25605714
39	RAD21	chr7:25603664-25607366	SK-N-SH	brain:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
40	CTCF	chr7:25605450-25605981	GM12878	blood:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
41	CTCF	chr7:25605315-25606065	T-47D	breast:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
42	RAD21	chr7:25605419-25605869	A549	lung:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
43	RAD21	chr7:25605380-25605940	HepG2	liver:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
44	CTCF	chr7:25604949-25606365	A549	lung:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
45	CTCF	chr7:25605394-25605913	A549	lung:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
46	CTCF	chr7:25605466-25605842	HepG2	liver:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
47	ATF3	chr7:25605508-25605772	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr7:25605421-25605882	A549	lung:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
49	RAD21	chr7:25605470-25605917	HepG2	liver:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
50	RUNX3	chr7:25605497-25605782	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:25433474..25434141-chr7:25605268..25606353,4	K562	blood:
2	chr7:25428818..25429573-chr7:25605415..25606098,2	K562	blood:
3	chr7:25596711..25599628-chr7:25603188..25605911,2	K562	blood:
4	chr7:25298973..25299854-chr7:25605283..25606167,4	MCF-7	breast:
5	chr7:25429055..25432240-chr7:25604579..25606349,45	MCF-7	breast:
6	chr7:25605406..25606179-chr7:25890948..25891905,5	K562	blood:
7	chr7:25432296..25432868-chr7:25605222..25605812,2	MCF-7	breast:
8	chr7:25430622..25431559-chr7:25605393..25606130,7	MCF-7	breast:
9	chr7:25605314..25606102-chr7:25891008..25891805,3	MCF-7	breast:
10	chr7:25428848..25430407-chr7:25605173..25606452,6	MCF-7	breast:
11	chr7:25433157..25433791-chr7:25605378..25606157,2	MCF-7	breast:
12	chr7:25298951..25300126-chr7:25605192..25606795,18	K562	blood:
13	chr7:25298470..25299852-chr7:25605228..25606576,11	MCF-7	breast:
14	chr7:25605147..25606187-chr7:25890189..25892015,14	MCF-7	breast:
15	chr7:25430463..25431643-chr7:25605112..25606187,14	K562	blood:

Variant related genes	Relation type
ENSG00000222101	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2938115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952521	0.82[ASN][1000 genomes]
rs2952524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999577	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	nsv522815	chr7:25599858-25606120	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv523322	chr7:25601480-25606120	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2952522	TAX1BP1	cis	cerebellum	SCAN
rs2952522	C7orf30	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25604000-25606000	Enhancers	Colon Smooth Muscle	Colon
2	chr7:25604000-25606200	Enhancers	Fetal Lung	lung
3	chr7:25604400-25605600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:25604400-25605600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:25604400-25605600	Enhancers	Rectal Smooth Muscle	rectum
6	chr7:25604400-25605600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr7:25604600-25605600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:25604600-25605600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:25604600-25605600	Enhancers	Adipose Nuclei	Adipose
10	chr7:25604600-25608200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:25604800-25608200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:25605200-25605600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:25605200-25605600	Enhancers	Fetal Brain Male	brain
14	chr7:25605200-25606400	Weak transcription	Fetal Stomach	stomach
15	chr7:25605200-25606800	Enhancers	Fetal Kidney	kidney
16	chr7:25605400-25605600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:25605400-25605600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr7:25605400-25605600	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr7:25605400-25605600	Enhancers	Duodenum Mucosa	Duodenum
20	chr7:25605400-25606000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr7:25605400-25606000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr7:25605400-25607000	Enhancers	Stomach Mucosa	stomach

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