Variant report

Variant	rs2074577
Chromosome Location	chr7:120611163-120611164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120609559..120611534-chr7:120718350..120721159,2	K562	blood:
2	chr7:120605248..120607980-chr7:120610074..120612153,2	MCF-7	breast:
3	chr7:120609328..120611534-chr7:120718016..120721159,3	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10085563	0.85[CEU][hapmap]
rs10252911	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs10272601	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs10277935	0.86[ASW][hapmap];0.83[LWK][hapmap]
rs10464522	0.81[ASN][1000 genomes]
rs10953922	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10953923	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs12706306	0.81[YRI][hapmap]
rs12706307	0.85[CEU][hapmap]
rs12706308	0.84[CEU][hapmap]
rs12706309	0.85[CEU][hapmap]
rs12706310	0.85[CEU][hapmap]
rs13881	0.85[CEU][hapmap]
rs1557857	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1859316	0.85[CHB][hapmap]
rs1859318	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1859319	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2058501	0.80[ASW][hapmap];0.96[LWK][hapmap]
rs2074576	0.95[CEU][hapmap]
rs2097806	0.81[YRI][hapmap]
rs2107276	0.85[CHB][hapmap]
rs2160010	0.85[CEU][hapmap]
rs2215786	0.85[CEU][hapmap]
rs2215789	0.85[CEU][hapmap]
rs2244863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248890	0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2525705	0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2525709	0.81[ASN][1000 genomes]
rs2525711	0.85[CEU][hapmap]
rs2525712	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]
rs2525713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525714	0.85[CEU][hapmap]
rs2525715	0.88[CEU][hapmap]
rs2525716	0.84[CEU][hapmap]
rs2525717	0.94[CEU][hapmap]
rs2525718	0.95[CEU][hapmap]
rs2525719	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525720	0.85[CEU][hapmap]
rs2525722	0.95[CEU][hapmap]
rs2525724	0.85[CEU][hapmap]
rs2525725	0.85[CEU][hapmap]
rs2525726	0.85[CEU][hapmap]
rs2525728	0.85[CEU][hapmap]
rs2525729	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2525730	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525733	0.85[CEU][hapmap]
rs2525734	0.85[CEU][hapmap]
rs2525735	0.85[CEU][hapmap]
rs2525736	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525737	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525738	0.85[CEU][hapmap]
rs2525739	0.89[CEU][hapmap]
rs2525740	0.85[CEU][hapmap]
rs2525741	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525743	0.81[ASN][1000 genomes]
rs2538485	0.85[CEU][hapmap]
rs2721326	0.85[CEU][hapmap]
rs2721336	0.85[CEU][hapmap]
rs2721337	0.85[CEU][hapmap]
rs2721340	0.85[CEU][hapmap]
rs2721341	0.93[ASW][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.96[LWK][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs2721345	0.85[CEU][hapmap]
rs2721350	0.84[CEU][hapmap]
rs2721351	0.95[CEU][hapmap]
rs2721354	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2721358	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721363	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721365	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721366	0.85[CEU][hapmap]
rs2721367	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721368	0.85[CEU][hapmap]
rs2721370	0.85[CEU][hapmap]
rs2721372	0.95[CEU][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757556	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap]
rs3823859	0.86[ASW][hapmap]
rs3944026	0.84[CEU][hapmap]
rs41688	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41689	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41690	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41691	0.85[CEU][hapmap]
rs41692	0.85[CEU][hapmap]
rs41694	0.85[CEU][hapmap]
rs41697	0.85[CEU][hapmap]
rs41703	0.85[CEU][hapmap]
rs41704	0.85[CEU][hapmap]
rs4727917	0.89[CEU][hapmap]
rs4730988	0.85[CEU][hapmap]
rs6466761	0.86[ASW][hapmap]
rs6466762	0.86[ASW][hapmap]
rs6466764	0.85[CEU][hapmap]
rs6944789	0.80[ASW][hapmap];0.96[LWK][hapmap]
rs6949989	0.86[ASW][hapmap];0.83[LWK][hapmap]
rs6964344	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs6966297	0.85[CEU][hapmap]
rs6970871	0.85[CEU][hapmap]
rs6971854	0.85[CHB][hapmap]
rs6973457	0.85[CEU][hapmap]
rs6979247	0.85[CHB][hapmap]
rs745167	0.81[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap]
rs7781985	0.86[ASW][hapmap]
rs7784837	0.85[CEU][hapmap]
rs7808593	0.85[CEU][hapmap]
rs996903	0.80[ASW][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2074577	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120611200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:120591600-120612800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:120591600-120613200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:120591600-120613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
6	chr7:120591800-120618600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:120592400-120614800	Weak transcription	Small Intestine	intestine
8	chr7:120592400-120617000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr7:120592400-120618600	Weak transcription	Right Ventricle	heart
10	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
11	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
12	chr7:120599600-120616200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:120601800-120613000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:120602600-120617200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:120602800-120615800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:120603000-120618000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr7:120603200-120618000	Strong transcription	Fetal Thymus	thymus
18	chr7:120603400-120617200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:120603600-120615400	Strong transcription	K562	blood
20	chr7:120603600-120616800	Strong transcription	Dnd41	blood
21	chr7:120604200-120613000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:120604200-120615800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:120604200-120617000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:120604400-120616800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr7:120604400-120617000	Strong transcription	Primary B cells from cord blood	blood
26	chr7:120604400-120617000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:120604400-120617200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:120604400-120617400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr7:120604400-120621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:120604600-120613400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:120604600-120615200	Strong transcription	GM12878-XiMat	blood
32	chr7:120604600-120615400	Strong transcription	Fetal Brain Female	brain
33	chr7:120604600-120615600	Strong transcription	Osteobl	bone
34	chr7:120604600-120616000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:120604600-120617000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr7:120604600-120617400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:120604600-120617400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr7:120604600-120617400	Strong transcription	Liver	Liver
39	chr7:120604600-120617400	Strong transcription	HSMM	muscle
40	chr7:120604800-120611600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:120604800-120611600	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:120604800-120611800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:120604800-120613800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:120604800-120614000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:120604800-120615600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:120604800-120616200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:120604800-120616400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:120604800-120616600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:120604800-120617000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:120604800-120617000	Strong transcription	Primary T cells fromperipheralblood	blood

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