Variant report

Variant	rs7871055
Chromosome Location	chr9:86245495-86245496
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86244611..86247023-chr9:86320465..86322962,2	MCF-7	breast:
2	chr9:86244110..86246714-chr9:86535414..86538304,2	K562	blood:
3	chr9:86243220..86245781-chr9:86323093..86324779,2	MCF-7	breast:
4	chr9:86230729..86232939-chr9:86244046..86245933,2	K562	blood:
5	chr9:86235832..86238192-chr9:86245437..86248685,3	K562	blood:
6	chr9:86243566..86245560-chr9:86258572..86260267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254473	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000148057	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10512136	0.90[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10512137	0.90[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs1056073	0.84[AMR][1000 genomes]
rs10746717	0.86[AMR][1000 genomes]
rs10780616	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780617	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10780618	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10780619	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10780620	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780622	0.86[AMR][1000 genomes]
rs10780623	0.84[AMR][1000 genomes]
rs10780624	0.82[AMR][1000 genomes]
rs10780625	0.94[CEU][hapmap];0.86[AMR][1000 genomes]
rs10868035	0.90[CEU][hapmap];0.88[AMR][1000 genomes]
rs10868036	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10868037	0.84[AMR][1000 genomes]
rs10868038	0.84[AMR][1000 genomes]
rs10868042	0.84[AMR][1000 genomes]
rs10868043	0.82[AMR][1000 genomes]
rs11140198	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs11140202	0.86[AMR][1000 genomes]
rs11140209	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11140212	0.90[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs11140221	0.86[AMR][1000 genomes]
rs11140223	0.80[AMR][1000 genomes]
rs11791175	0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1333861	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1333862	0.90[CEU][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1537502	0.90[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1537503	0.92[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1961941	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2282220	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2780975	0.86[CHB][hapmap]
rs2780982	0.85[CHB][hapmap]
rs2811917	0.89[LWK][hapmap]
rs2811921	0.82[YRI][hapmap]
rs2811927	0.83[CHB][hapmap]
rs3750409	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3750410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814505	0.90[CEU][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4146740	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4454364	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4877790	0.90[AMR][1000 genomes]
rs4877791	0.90[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs4877793	0.86[AMR][1000 genomes]
rs4877794	0.89[CEU][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs4877796	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4877797	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs4877799	0.89[CEU][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4877800	0.83[AMR][1000 genomes]
rs7046388	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72618136	0.86[AMR][1000 genomes]
rs7860614	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7863266	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7866234	0.90[CEU][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs868917	0.90[CEU][hapmap];0.86[AMR][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv973848	chr9:86241130-86260149	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7871055	RP11-522I20.3	cis	Whole Blood	GTEx
rs7871055	RP11-522I20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86238600-86265000	Weak transcription	Ovary	ovary
2	chr9:86238800-86246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:86238800-86246000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:86238800-86254600	Weak transcription	Left Ventricle	heart
5	chr9:86238800-86260600	Weak transcription	Right Ventricle	heart
6	chr9:86238800-86264600	Weak transcription	Psoas Muscle	Psoas
7	chr9:86239000-86250000	Weak transcription	HSMMtube	muscle
8	chr9:86239000-86264800	Weak transcription	HMEC	breast
9	chr9:86239000-86265200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:86239200-86245800	Weak transcription	Brain Germinal Matrix	brain
11	chr9:86239200-86261000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:86239400-86245800	Weak transcription	Fetal Heart	heart
13	chr9:86239400-86245800	Weak transcription	Fetal Lung	lung
14	chr9:86239400-86248000	Weak transcription	NHDF-Ad	bronchial
15	chr9:86239400-86254400	Weak transcription	Brain Anterior Caudate	brain
16	chr9:86239400-86254400	Weak transcription	Brain Substantia Nigra	brain
17	chr9:86239400-86266200	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:86239400-86266400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:86239600-86245600	Weak transcription	Brain Angular Gyrus	brain
20	chr9:86239600-86245600	Weak transcription	Fetal Brain Female	brain
21	chr9:86239600-86260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:86239600-86260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:86239600-86265000	Weak transcription	HUVEC	blood vessel
24	chr9:86239600-86266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:86239800-86266800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:86240000-86246000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:86240200-86265000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:86240400-86254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:86240600-86245800	Weak transcription	K562	blood
31	chr9:86242200-86256600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:86242400-86246000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:86242400-86253800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:86242400-86257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:86242400-86264800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr9:86242600-86265000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr9:86243200-86245600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:86243200-86260800	Weak transcription	Primary B cells from cord blood	blood
39	chr9:86243200-86261000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:86243200-86269600	Weak transcription	Pancreas	Pancrea
41	chr9:86243600-86246000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr9:86243600-86264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:86243600-86266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr9:86244000-86246000	Enhancers	Duodenum Mucosa	Duodenum
45	chr9:86244000-86246600	Enhancers	Placenta	Placenta
46	chr9:86244000-86260600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr9:86244000-86260800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr9:86244200-86245800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:86244200-86246000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:86244200-86264600	Weak transcription	Rectal Mucosa Donor 29	rectum

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