Variant report

Variant	rs2402972
Chromosome Location	chr7:129381953-129381954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129380254..129382975-chr7:129414293..129416363,2	K562	blood:
2	chr7:129381004..129383973-chr7:129384004..129385791,2	K562	blood:
3	chr7:129379929..129382728-chr7:129402086..129404067,3	K562	blood:
4	chr7:129374523..129378775-chr7:129380102..129386585,8	K562	blood:
5	chr7:129380203..129383393-chr7:129464866..129467037,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199158	Chromatin interaction
ENSG00000207691	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10215964	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10245497	1.00[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[YRI][hapmap]
rs10255077	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275592	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10808240	1.00[CHB][hapmap]
rs1450878	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1562833	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1732008	0.80[YRI][hapmap]
rs2402961	0.81[AFR][1000 genomes]
rs2402966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2402968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2402969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402978	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896422	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896423	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292630	1.00[CHB][hapmap]
rs4728171	0.85[CHB][hapmap]
rs4728177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731608	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4731612	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4731621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58736446	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6467255	0.86[CHB][hapmap]
rs6467257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs6949469	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949742	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958958	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967348	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7778085	1.00[CHB][hapmap]
rs7794909	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801252	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802940	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7805465	1.00[CHB][hapmap]
rs7809459	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792084	1.00[CHB][hapmap];0.88[CHD][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	esv1813824	chr7:129379450-129424461	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	364 gene(s)	inside rSNPs	diseases
2	esv14232	chr7:129379923-129445465	Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	365 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129348200-129392000	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:129351600-129394800	Weak transcription	Hela-S3	cervix
3	chr7:129357000-129392400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:129360600-129394800	Weak transcription	Small Intestine	intestine
5	chr7:129361800-129392400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:129362200-129387800	Strong transcription	Liver	Liver
7	chr7:129364200-129397600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:129365200-129388400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:129366800-129399400	Weak transcription	Fetal Kidney	kidney
10	chr7:129369600-129399400	Weak transcription	Fetal Brain Male	brain
11	chr7:129372000-129383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:129372000-129390000	Weak transcription	HMEC	breast
13	chr7:129372200-129387000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:129372200-129390000	Weak transcription	NHEK	skin
15	chr7:129372200-129397800	Weak transcription	NH-A	brain
16	chr7:129372400-129398800	Weak transcription	NHLF	lung
17	chr7:129373400-129389200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:129373600-129385600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:129373800-129385200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr7:129373800-129392000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr7:129374600-129394800	Weak transcription	Gastric	stomach
22	chr7:129374800-129386600	Weak transcription	Esophagus	oesophagus
23	chr7:129374800-129390000	Weak transcription	Colonic Mucosa	Colon
24	chr7:129375000-129386600	Weak transcription	GM12878-XiMat	blood
25	chr7:129375000-129390000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:129375000-129391600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:129375000-129394800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:129375000-129395400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:129375800-129392000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:129376600-129384600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:129376600-129393000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr7:129376600-129397200	Strong transcription	Dnd41	blood
33	chr7:129376800-129383600	Enhancers	Fetal Heart	heart
34	chr7:129376800-129392200	Strong transcription	Primary T cells from cord blood	blood
35	chr7:129377000-129382200	Strong transcription	Primary B cells from cord blood	blood
36	chr7:129377000-129387800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:129377200-129387200	Strong transcription	Fetal Stomach	stomach
38	chr7:129377200-129392800	Strong transcription	Thymus	Thymus
39	chr7:129377400-129382200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:129377600-129382400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:129377600-129382400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr7:129377600-129387600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:129377800-129382400	Genic enhancers	Fetal Muscle Leg	muscle
44	chr7:129378000-129382800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:129378000-129383400	Enhancers	Brain Cingulate Gyrus	brain
46	chr7:129378400-129382000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:129378400-129386600	Weak transcription	Fetal Lung	lung
48	chr7:129378600-129383400	Enhancers	Brain Substantia Nigra	brain
49	chr7:129378600-129383800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:129378800-129383400	Enhancers	Brain Angular Gyrus	brain

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