Variant report

Variant	rs2127096
Chromosome Location	chr17:20934127-20934128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20930509..20934223-chr17:20943543..20949021,6	MCF-7	breast:
2	chr17:20932232..20934940-chr17:20938795..20941578,2	MCF-7	breast:
3	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:
4	chr17:20923362..20925822-chr17:20932717..20934494,2	K562	blood:
5	chr17:20913654..20920338-chr17:20930133..20937587,8	K562	blood:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10153263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512422	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11541314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650653	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869201	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869217	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869959	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450389	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452171	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937950	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12947514	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962364	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1871275	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28663143	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2886049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354508	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35022634	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4381653	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427861	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985942	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985945	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55633111	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57522885	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587107	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587113	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587116	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66487709	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66516868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73303698	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8072149	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080321	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs984007	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893047	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895277	1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895618	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896853	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9907786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914758	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914916	0.81[EUR][1000 genomes];0.82[ASN][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	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2127096	SMCR7	cis	cerebellum	SCAN
rs2127096	RP11-381P6.1	cis	Muscle Skeletal	GTEx
rs2127096	ALDH3A1	cis	cerebellum	SCAN
rs2127096	USP22	cis	lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:20902000-20935400	Strong transcription	Dnd41	blood
4	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:20926200-20934200	Strong transcription	K562	blood
8	chr17:20929800-20935200	Weak transcription	Fetal Kidney	kidney
9	chr17:20930200-20935600	Strong transcription	GM12878-XiMat	blood
10	chr17:20930600-20935400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:20931600-20935400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:20931600-20937600	Enhancers	Brain Substantia Nigra	brain
13	chr17:20931800-20934400	Enhancers	Colon Smooth Muscle	Colon
14	chr17:20931800-20935200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr17:20931800-20935400	Enhancers	Fetal Heart	heart
16	chr17:20931800-20936600	Weak transcription	HUVEC	blood vessel
17	chr17:20931800-20937000	Genic enhancers	HSMM	muscle
18	chr17:20931800-20940200	Enhancers	Brain Cingulate Gyrus	brain
19	chr17:20932000-20935000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:20932000-20935000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:20932000-20935200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr17:20932000-20935400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr17:20932000-20935600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:20932000-20936400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:20932000-20936400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:20932000-20936600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr17:20932000-20937400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr17:20932000-20937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr17:20932000-20937400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr17:20932000-20938000	Enhancers	Brain Hippocampus Middle	brain
31	chr17:20932200-20934400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr17:20932200-20934600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr17:20932200-20935000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr17:20932200-20935200	Enhancers	Fetal Lung	lung
35	chr17:20932200-20936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:20932200-20936400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:20932200-20936400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:20932200-20937400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr17:20932200-20937800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr17:20932200-20941400	Genic enhancers	A549	lung
41	chr17:20932400-20934200	Enhancers	Fetal Brain Male	brain
42	chr17:20932400-20934600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:20932400-20935200	Weak transcription	Fetal Thymus	thymus
44	chr17:20932400-20935400	Weak transcription	Fetal Intestine Small	intestine
45	chr17:20932400-20935400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr17:20932400-20935400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr17:20932400-20935600	Weak transcription	Placenta	Placenta
48	chr17:20932400-20935800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr17:20932400-20935800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:20932400-20936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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