Variant report

Variant	rs2721368
Chromosome Location	chr7:120613537-120613538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120611920..120613871-chr7:120614281..120617213,2	K562	blood:
2	chr7:120611698..120613839-chr7:120717573..120721015,3	K562	blood:
3	chr7:120611633..120614559-chr7:120625777..120628879,3	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10258025	0.81[EUR][1000 genomes]
rs11363	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.81[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525718	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525719	0.90[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525722	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525724	1.00[CEU][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]
rs2525725	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2525726	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]
rs2525728	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]
rs2525731	0.94[EUR][1000 genomes]
rs2525732	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];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];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525734	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]
rs2525735	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2525739	1.00[CEU][hapmap]
rs2525740	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs2721350	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721366	1.00[CEU][hapmap];1.00[CHB][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]
rs2721370	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2721372	0.90[CEU][hapmap]
rs2896299	0.84[CEU][hapmap]
rs3944026	1.00[CEU][hapmap];0.85[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];0.81[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4727915	0.84[CEU][hapmap]
rs4730985	0.83[CEU][hapmap]
rs6966297	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7808535	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]

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
rs2721368	SPAM1	cis	parietal	SCAN
rs2721368	KCND2	cis	cerebellum	SCAN
rs2721368	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 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	chr7:120592400-120614800	Weak transcription	Small Intestine	intestine
4	chr7:120592400-120617000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr7:120592400-120618600	Weak transcription	Right Ventricle	heart
6	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
7	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
8	chr7:120599600-120616200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:120602600-120617200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:120602800-120615800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:120603000-120618000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr7:120603200-120618000	Strong transcription	Fetal Thymus	thymus
13	chr7:120603400-120617200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:120603600-120615400	Strong transcription	K562	blood
15	chr7:120603600-120616800	Strong transcription	Dnd41	blood
16	chr7:120604200-120615800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:120604200-120617000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:120604400-120616800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr7:120604400-120617000	Strong transcription	Primary B cells from cord blood	blood
20	chr7:120604400-120617000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:120604400-120617200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:120604400-120617400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr7:120604400-120621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:120604600-120615200	Strong transcription	GM12878-XiMat	blood
25	chr7:120604600-120615400	Strong transcription	Fetal Brain Female	brain
26	chr7:120604600-120615600	Strong transcription	Osteobl	bone
27	chr7:120604600-120616000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:120604600-120617000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr7:120604600-120617400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:120604600-120617400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr7:120604600-120617400	Strong transcription	Liver	Liver
32	chr7:120604600-120617400	Strong transcription	HSMM	muscle
33	chr7:120604800-120613800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:120604800-120614000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:120604800-120615600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:120604800-120616200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:120604800-120616400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:120604800-120616600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:120604800-120617000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr7:120604800-120617000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr7:120604800-120617200	Strong transcription	Adipose Nuclei	Adipose
42	chr7:120604800-120617200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr7:120604800-120617400	Strong transcription	Placenta	Placenta
44	chr7:120604800-120617400	Strong transcription	HUVEC	blood vessel
45	chr7:120605000-120617000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:120605600-120615800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:120606000-120617200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:120606400-120615600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:120606400-120616200	Strong transcription	Fetal Intestine Large	intestine
50	chr7:120606600-120615600	Strong transcription	Colon Smooth Muscle	Colon

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