Variant report

Variant	rs2525735
Chromosome Location	chr7:120625264-120625265
allele	A/C
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	ATF3	chr7:120625163-120625596	K562	blood:	n/a	chr7:120625406-120625417 chr7:120625404-120625414 chr7:120625405-120625416 chr7:120625407-120625415 chr7:120625403-120625418 chr7:120625406-120625414 chr7:120625404-120625415 chr7:120625405-120625418 chr7:120625407-120625414 chr7:120625404-120625417 chr7:120625404-120625414 chr7:120625407-120625417
2	MAFF	chr7:120624931-120625500	K562	blood:	n/a	n/a
3	MAZ	chr7:120625156-120625599	K562	blood:	n/a	n/a
4	CTCF	chr7:120625260-120625410	HEEpiC	esophagus:	n/a	n/a
5	JUND	chr7:120625084-120625695	K562	blood:	n/a	chr7:120625406-120625415
6	STAT5A	chr7:120625143-120625482	K562	blood:	n/a	n/a
7	CEBPD	chr7:120625097-120625673	K562	blood:	n/a	n/a
8	JUND	chr7:120625223-120625589	HepG2	liver:	n/a	chr7:120625406-120625415
9	TBL1XR1	chr7:120625164-120625600	K562	blood:	n/a	n/a
10	IRF1	chr7:120625156-120625554	K562	blood:	n/a	chr7:120625466-120625476
11	GATA3	chr7:120625167-120625702	SK-N-SH	brain:	n/a	chr7:120625298-120625305 chr7:120625298-120625305 chr7:120625379-120625388 chr7:120625298-120625305 chr7:120625376-120625392
12	IRF1	chr7:120625065-120625583	K562	blood:	n/a	chr7:120625466-120625476
13	NR2F2	chr7:120625122-120625745	K562	blood:	n/a	n/a
14	CEBPD	chr7:120625064-120625647	K562	blood:	n/a	n/a
15	UBTF	chr7:120625211-120625532	K562	blood:	n/a	n/a
16	STAT3	chr7:120625260-120625551	Hela-S3	cervix:	n/a	n/a
17	MAFK	chr7:120625109-120625533	K562	blood:	n/a	n/a
18	TRIM28	chr7:120624976-120625709	K562	blood:	n/a	n/a
19	CCNT2	chr7:120625179-120625604	K562	blood:	n/a	n/a
20	JUN	chr7:120625192-120625592	K562	blood:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
21	ARID3A	chr7:120625154-120625590	K562	blood:	n/a	n/a
22	GATA2	chr7:120625127-120625860	SH-SY5Y	brain:	n/a	chr7:120625298-120625305 chr7:120625298-120625305 chr7:120625379-120625388 chr7:120625298-120625305 chr7:120625376-120625392
23	JUN	chr7:120625141-120625598	K562	blood:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
24	YY1	chr7:120625175-120625560	SK-N-SH_RA	brain:	n/a	n/a
25	TEAD4	chr7:120624918-120625741	K562	blood:	n/a	n/a
26	GATA3	chr7:120625146-120625754	SH-SY5Y	brain:	n/a	chr7:120625298-120625305 chr7:120625298-120625305 chr7:120625379-120625388 chr7:120625298-120625305 chr7:120625376-120625392
27	JUN	chr7:120625144-120625664	K562	blood:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
28	TAL1	chr7:120625165-120625584	K562	blood:	n/a	chr7:120625298-120625306
29	ATF1	chr7:120625059-120625590	K562	blood:	n/a	n/a
30	GATA2	chr7:120625157-120625573	K562	blood:	n/a	chr7:120625298-120625305 chr7:120625298-120625305 chr7:120625379-120625388 chr7:120625298-120625305 chr7:120625376-120625392
31	TEAD4	chr7:120624989-120625585	K562	blood:	n/a	n/a
32	POLR2A	chr7:120625233-120625505	SK-N-SH	brain:	n/a	n/a
33	CUX1	chr7:120625134-120625756	K562	blood:	n/a	n/a
34	JUND	chr7:120624479-120625812	SK-N-SH	brain:	n/a	chr7:120625406-120625415
35	CREB1	chr7:120624400-120625930	K562	blood:	n/a	chr7:120625404-120625417
36	EP300	chr7:120624468-120626977	SK-N-SH	brain:	n/a	chr7:120625228-120625235 chr7:120626631-120626641
37	REST	chr7:120625255-120625510	SK-N-SH	brain:	n/a	n/a
38	MYC	chr7:120625140-120625601	K562	blood:	n/a	n/a
39	JUN	chr7:120625232-120625592	HepG2	liver:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
40	JUN	chr7:120625125-120625620	K562	blood:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
41	EP300	chr7:120625100-120625724	SK-N-SH_RA	brain:	n/a	chr7:120625228-120625235
42	EP300	chr7:120625126-120625691	SK-N-SH_RA	brain:	n/a	chr7:120625228-120625235
43	EP300	chr7:120625121-120625593	K562	blood:	n/a	chr7:120625228-120625235
44	IRF1	chr7:120625142-120625543	K562	blood:	n/a	chr7:120625466-120625476
45	JUN	chr7:120625157-120625616	K562	blood:	n/a	chr7:120625405-120625418 chr7:120625406-120625415
46	GATA3	chr7:120625018-120625794	SK-N-SH	brain:	n/a	chr7:120625298-120625305 chr7:120625298-120625305 chr7:120625379-120625388 chr7:120625298-120625305 chr7:120625376-120625392
47	RCOR1	chr7:120625043-120625899	K562	blood:	n/a	n/a
48	BRCA1	chr7:120625247-120625518	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:120624272..120626644-chr7:120740738..120743095,2	K562	blood:
2	chr7:120622642..120624338-chr7:120624667..120626865,2	K562	blood:
3	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
4	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
RNA5SP240	TF binding region
CPED1	TF binding region
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10229719	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10258025	0.93[EUR][1000 genomes]
rs11363	0.84[EUR][1000 genomes]
rs12672149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13881	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs193727	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2013083	0.82[AMR][1000 genomes]
rs2013087	0.84[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs2074576	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2074577	0.85[CEU][hapmap]
rs2215786	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2215789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525717	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525718	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525722	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525723	0.82[EUR][1000 genomes]
rs2525724	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525728	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2525731	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2525732	0.85[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2525736	0.85[EUR][1000 genomes]
rs2525738	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2525740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2525741	0.82[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2721358	0.82[EUR][1000 genomes]
rs2721359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2721361	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2721363	0.83[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2721368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2721370	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3944026	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs41689	0.82[EUR][1000 genomes]
rs41691	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41693	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41694	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41695	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41697	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41703	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4730987	0.82[AMR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6973457	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7789501	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7808535	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.83[EUR][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	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2525735	SPAM1	cis	parietal	SCAN
rs2525735	TSPAN12	cis	Artery Tibial	GTEx
rs2525735	FLJ21986	cis	multi-tissue	Pritchard
rs2525735	KCND2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
2	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
3	chr7:120608600-120627600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:120609400-120627800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:120609400-120627800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:120609400-120628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:120611600-120626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:120611600-120627400	Weak transcription	Brain Angular Gyrus	brain
9	chr7:120611600-120627600	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:120611600-120627600	Weak transcription	Fetal Stomach	stomach
11	chr7:120611600-120627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:120611600-120627800	Weak transcription	Esophagus	oesophagus
13	chr7:120611600-120627800	Weak transcription	Thymus	Thymus
14	chr7:120615000-120627600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:120615400-120627800	Weak transcription	Colonic Mucosa	Colon
16	chr7:120615400-120628000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:120615600-120627400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:120615600-120627600	Weak transcription	Brain Anterior Caudate	brain
19	chr7:120615600-120627800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:120615600-120627800	Weak transcription	Colon Smooth Muscle	Colon
21	chr7:120615600-120627800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:120615600-120628000	Weak transcription	Small Intestine	intestine
23	chr7:120615800-120627800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:120616000-120627400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:120616000-120627600	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:120616200-120627400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:120616200-120627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:120616200-120627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:120616200-120627800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:120616200-120627800	Weak transcription	Fetal Intestine Large	intestine
31	chr7:120616600-120627600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:120616600-120627600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:120616800-120628000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:120617000-120627000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:120617000-120627800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr7:120617000-120627800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:120617200-120627800	Weak transcription	Adipose Nuclei	Adipose
38	chr7:120617200-120627800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:120617200-120627800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr7:120617200-120627800	Weak transcription	Left Ventricle	heart
41	chr7:120617400-120627800	Weak transcription	Liver	Liver
42	chr7:120617400-120627800	Weak transcription	Placenta	Placenta
43	chr7:120617400-120627800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:120617400-120627800	Weak transcription	HUVEC	blood vessel
45	chr7:120618000-120627800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr7:120620400-120627800	Weak transcription	Right Atrium	heart
47	chr7:120620800-120628600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr7:120622000-120627600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:120622000-120627800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:120622200-120625800	Weak transcription	H1 Cell Line	embryonic stem cell

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