Variant report

Variant	rs2525734
Chromosome Location	chr7:120624165-120624166
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	RFX5	chr7:120624129-120624320	K562	blood:	n/a	n/a
2	TBL1XR1	chr7:120624121-120624214	K562	blood:	n/a	n/a
3	CEBPB	chr7:120624091-120624357	K562	blood:	n/a	chr7:120624218-120624229 chr7:120624218-120624231

No.	Distal block	Cell Line	Cell type
1	chr7:120622360..120624789-chr7:120627445..120629429,3	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
CPED1	TF binding region
RNA5SP240	TF binding region
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10229719	0.82[EUR][1000 genomes]
rs10258025	0.84[EUR][1000 genomes]
rs11363	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12672149	0.81[EUR][1000 genomes]
rs13881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193727	0.81[EUR][1000 genomes]
rs2013087	0.84[CEU][hapmap]
rs2074576	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074577	0.85[CEU][hapmap]
rs2215786	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2215789	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2244863	0.85[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525718	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525722	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525723	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525725	1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525731	0.97[EUR][1000 genomes]
rs2525732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525735	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525740	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2721359	0.82[EUR][1000 genomes]
rs2721361	0.82[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2721368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2721370	1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs3944026	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap]
rs41691	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs41692	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs41693	0.81[EUR][1000 genomes]
rs41694	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs41695	0.81[EUR][1000 genomes]
rs41697	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs41703	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7789501	0.82[EUR][1000 genomes]
rs7808535	0.84[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.82[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
rs2525734	SPAM1	cis	parietal	SCAN
rs2525734	TSPAN12	cis	Artery Tibial	GTEx
rs2525734	KCND2	cis	cerebellum	SCAN
rs2525734	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 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	chr7:120615600-120624400	Weak transcription	Hela-S3	cervix
18	chr7:120615600-120627400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:120615600-120627600	Weak transcription	Brain Anterior Caudate	brain
20	chr7:120615600-120627800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:120615600-120627800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:120615600-120627800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:120615600-120628000	Weak transcription	Small Intestine	intestine
24	chr7:120615800-120627800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:120616000-120627400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:120616000-120627600	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:120616200-120627400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:120616200-120627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:120616200-120627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:120616200-120627800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr7:120616200-120627800	Weak transcription	Fetal Intestine Large	intestine
32	chr7:120616600-120627600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:120616600-120627600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:120616800-120628000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:120617000-120627000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:120617000-120627800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr7:120617000-120627800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:120617200-120627800	Weak transcription	Adipose Nuclei	Adipose
39	chr7:120617200-120627800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:120617200-120627800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:120617200-120627800	Weak transcription	Left Ventricle	heart
42	chr7:120617400-120624800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:120617400-120627800	Weak transcription	Liver	Liver
44	chr7:120617400-120627800	Weak transcription	Placenta	Placenta
45	chr7:120617400-120627800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:120617400-120627800	Weak transcription	HUVEC	blood vessel
47	chr7:120618000-120627800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:120620400-120627800	Weak transcription	Right Atrium	heart
49	chr7:120620800-120628600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr7:120621800-120625000	Enhancers	K562	blood

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