Variant report

Variant	rs2525728
Chromosome Location	chr7:120617749-120617750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120616082..120617788-chr7:120647461..120650370,2	K562	blood:
2	chr7:120617320..120619610-chr7:120694736..120697163,2	K562	blood:
3	chr7:120614613..120620636-chr7:120722021..120725742,5	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10229719	0.81[EUR][1000 genomes]
rs10258025	0.83[EUR][1000 genomes]
rs11363	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074577	0.85[CEU][hapmap]
rs2215786	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2215789	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
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];0.99[EUR][1000 genomes];1.00[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];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525723	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525725	1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.96[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525731	0.96[EUR][1000 genomes]
rs2525732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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]
rs2525734	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]
rs2525735	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525740	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721359	0.81[EUR][1000 genomes]
rs2721361	0.81[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721370	1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap]
rs3944026	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs41688	0.85[CEU][hapmap]
rs41691	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs41692	1.00[CEU][hapmap]
rs41694	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs41697	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs41703	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4730985	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs7789501	0.81[EUR][1000 genomes]
rs7808535	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2525728	KCND2	cis	cerebellum	SCAN
rs2525728	SPAM1	cis	parietal	SCAN
rs2525728	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
2	chr7:120591800-120618600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:120592400-120618600	Weak transcription	Right Ventricle	heart
4	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
5	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
6	chr7:120603000-120618000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:120603200-120618000	Strong transcription	Fetal Thymus	thymus
8	chr7:120604400-120621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:120608200-120621800	Weak transcription	NHEK	skin
10	chr7:120608600-120627600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:120609400-120622400	Weak transcription	Gastric	stomach
12	chr7:120609400-120627800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:120609400-120627800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:120609400-120628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:120611600-120619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:120611600-120619400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:120611600-120620000	Weak transcription	Fetal Heart	heart
18	chr7:120611600-120621800	Weak transcription	HMEC	breast
19	chr7:120611600-120622000	Weak transcription	Fetal Intestine Small	intestine
20	chr7:120611600-120622200	Weak transcription	HSMMtube	muscle
21	chr7:120611600-120624000	Weak transcription	Fetal Brain Male	brain
22	chr7:120611600-120626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:120611600-120627400	Weak transcription	Brain Angular Gyrus	brain
24	chr7:120611600-120627600	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:120611600-120627600	Weak transcription	Fetal Stomach	stomach
26	chr7:120611600-120627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:120611600-120627800	Weak transcription	Esophagus	oesophagus
28	chr7:120611600-120627800	Weak transcription	Thymus	Thymus
29	chr7:120611800-120619800	Weak transcription	A549	lung
30	chr7:120611800-120620200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:120611800-120620400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:120611800-120621800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:120612000-120618600	Weak transcription	Brain Germinal Matrix	brain
34	chr7:120613600-120618000	Strong transcription	Primary T cells from cord blood	blood
35	chr7:120615000-120627600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:120615200-120618800	Weak transcription	Psoas Muscle	Psoas
37	chr7:120615200-120619600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:120615200-120621800	Weak transcription	GM12878-XiMat	blood
39	chr7:120615400-120618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:120615400-120619000	Weak transcription	Fetal Kidney	kidney
41	chr7:120615400-120619200	Weak transcription	NHDF-Ad	bronchial
42	chr7:120615400-120619600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:120615400-120619800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:120615400-120620400	Weak transcription	Fetal Brain Female	brain
45	chr7:120615400-120621800	Weak transcription	K562	blood
46	chr7:120615400-120627800	Weak transcription	Colonic Mucosa	Colon
47	chr7:120615400-120628000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:120615600-120618000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr7:120615600-120619000	Weak transcription	Fetal Lung	lung
50	chr7:120615600-120619200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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