Variant report

Variant	rs2402947
Chromosome Location	chr7:128911322-128911323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128863320..128866916-chr7:128907366..128912174,7	MCF-7	breast:
2	chr7:128857969..128858990-chr7:128911282..128912153,7	MCF-7	breast:
3	chr7:128904465..128906876-chr7:128909348..128911601,2	K562	blood:
4	chr7:128858132..128859063-chr7:128911285..128912259,10	K562	blood:
5	chr7:128909835..128912504-chr7:128923384..128925064,2	K562	blood:
6	chr7:128911298..128913685-chr7:128916132..128918074,2	K562	blood:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10215998	1.00[EUR][1000 genomes]
rs10235589	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10249336	0.81[AFR][1000 genomes]
rs10255583	0.87[AFR][1000 genomes]
rs10264209	0.81[LWK][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs10269495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10281269	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12533108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13240723	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs1405475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1469554	1.00[EUR][1000 genomes]
rs1526898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1526899	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1549788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1609043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2052962	0.87[AMR][1000 genomes]
rs2402946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2463096	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2566875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2566881	1.00[MEX][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs2566882	0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs2694570	0.87[AFR][1000 genomes]
rs2694575	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694576	0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs2694577	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694583	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694591	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718090	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718091	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718092	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718097	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28399138	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437865	0.87[AMR][1000 genomes]
rs28475451	0.87[AMR][1000 genomes]
rs28864519	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2896414	0.94[AFR][1000 genomes]
rs4731567	1.00[EUR][1000 genomes]
rs6467234	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6467236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6467239	0.81[AFR][1000 genomes]
rs6949882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950279	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950496	0.89[AFR][1000 genomes]
rs6970267	0.95[AFR][1000 genomes]
rs71529418	0.91[AFR][1000 genomes]
rs71577870	0.91[AFR][1000 genomes]
rs7805353	0.87[AMR][1000 genomes]
rs9641847	0.82[ASW][hapmap];1.00[EUR][1000 genomes]
rs9641848	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349195	chr7:128887559-128918489	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128892600-128914200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:128897400-128914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:128897400-128919400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:128898800-128919600	Weak transcription	Right Ventricle	heart
5	chr7:128899000-128911600	Weak transcription	Brain Anterior Caudate	brain
6	chr7:128899400-128913600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:128900000-128925000	Weak transcription	Psoas Muscle	Psoas
8	chr7:128902200-128913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:128902600-128911800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:128902600-128914200	Weak transcription	Esophagus	oesophagus
11	chr7:128902600-128914200	Weak transcription	Gastric	stomach
12	chr7:128902600-128934000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:128902800-128914000	Weak transcription	Primary T cells from cord blood	blood
14	chr7:128902800-128928600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:128903000-128929200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:128903200-128913400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:128903200-128914200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:128903200-128925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:128903400-128931400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:128903400-128933800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:128903600-128913600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:128905200-128922800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:128905800-128932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:128906000-128914000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:128906400-128913200	Weak transcription	Fetal Intestine Small	intestine
26	chr7:128906400-128913400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:128906400-128913800	Weak transcription	HMEC	breast
28	chr7:128906600-128913800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:128907600-128913800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:128907800-128924400	Weak transcription	Small Intestine	intestine
31	chr7:128909200-128911800	Weak transcription	Pancreas	Pancrea
32	chr7:128909800-128911600	Enhancers	Primary B cells from cord blood	blood
33	chr7:128909800-128912000	Enhancers	Primary hematopoietic stem cells	blood
34	chr7:128909800-128925600	Weak transcription	Left Ventricle	heart
35	chr7:128910000-128911600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:128910000-128912400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:128910200-128924800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:128910400-128911400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr7:128910400-128914200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:128910600-128913400	Weak transcription	NHEK	skin
41	chr7:128910600-128913600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:128910800-128911800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:128910800-128913400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:128911000-128911600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:128911000-128913600	Weak transcription	GM12878-XiMat	blood
46	chr7:128911000-128913800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:128911000-128934400	Weak transcription	Brain Angular Gyrus	brain
48	chr7:128911200-128911400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr7:128911200-128911600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr7:128911200-128912200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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