Variant report

Variant	rs2240572
Chromosome Location	chr7:12610594-12610595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12608764..12610772-chr7:12727255..12728888,2	K562	blood:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1034856	0.89[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1118998	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11558844	0.85[EUR][1000 genomes]
rs11973033	0.96[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283717	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs17355921	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1990224	0.96[CEU][hapmap]
rs1990225	0.96[CEU][hapmap]
rs2240574	0.93[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs3735222	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735223	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41356146	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41379149	0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs4458754	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55682719	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55829483	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55999874	0.99[ASN][1000 genomes]
rs56085455	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56274604	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56760264	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57710906	0.81[AMR][1000 genomes]
rs57778115	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57805173	0.80[AMR][1000 genomes]
rs6460964	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460965	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6954111	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6961909	0.82[EUR][1000 genomes]
rs6965970	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967031	0.88[JPT][hapmap]
rs6972418	0.99[ASN][1000 genomes]
rs73060662	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73060664	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73060678	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73060679	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73060680	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73060684	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73060686	0.99[ASN][1000 genomes]
rs73062610	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73062611	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73062639	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7782451	0.96[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7799976	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7803810	0.96[CEU][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7804260	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7811582	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528031	chr7:12536336-12618764	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1025397	chr7:12543161-12612059	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1025006	chr7:12543161-12618924	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027831	chr7:12543161-12619740	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv470066	chr7:12543794-12618764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033478	chr7:12547121-12618924	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv464379	chr7:12572742-12618764	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv606231	chr7:12572742-12618764	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2240572	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12609400-12610600	Active TSS	Hela-S3	cervix
2	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:12609400-12611000	Enhancers	Spleen	Spleen
4	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
5	chr7:12609400-12611600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr7:12609600-12610600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
7	chr7:12609600-12610600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:12609600-12610800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
9	chr7:12609600-12611000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
10	chr7:12609600-12611200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:12609600-12611200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr7:12609600-12611200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:12609600-12612000	Active TSS	Brain Anterior Caudate	brain
14	chr7:12609800-12610600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr7:12609800-12610600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
16	chr7:12609800-12610600	Flanking Active TSS	HMEC	breast
17	chr7:12609800-12610800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
18	chr7:12609800-12610800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:12609800-12610800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
20	chr7:12609800-12610800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr7:12609800-12610800	Active TSS	Right Atrium	heart
22	chr7:12609800-12610800	Flanking Bivalent TSS/Enh	Osteobl	bone
23	chr7:12609800-12611000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:12609800-12611000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
28	chr7:12609800-12611000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:12609800-12611000	Bivalent Enhancer	Liver	Liver
31	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr7:12609800-12611000	Active TSS	K562	blood
35	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	NH-A	brain
37	chr7:12609800-12611200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr7:12609800-12611200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr7:12609800-12611200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr7:12609800-12611200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr7:12609800-12611200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
42	chr7:12609800-12611200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
43	chr7:12609800-12611600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
44	chr7:12610000-12610600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:12610000-12610600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:12610000-12610600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
47	chr7:12610000-12610600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr7:12610000-12610600	Active TSS	Aorta	Aorta
49	chr7:12610000-12610600	Flanking Active TSS	Placenta	Placenta
50	chr7:12610000-12610600	Active TSS	Gastric	stomach

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