Variant report

Variant	rs12160891
Chromosome Location	chr22:28256019-28256020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs138644	0.87[JPT][hapmap]
rs2073028	0.81[JPT][hapmap];1.00[MEX][hapmap]
rs2143180	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267123	0.85[CHD][hapmap]
rs2267125	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2345019	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28372773	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5752651	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752670	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5762398	0.80[AMR][1000 genomes]
rs5762400	0.94[AFR][1000 genomes]
rs5762404	0.88[CHD][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs5762410	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5762412	0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5762425	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5762428	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5997318	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997320	0.81[ASN][1000 genomes]
rs6005674	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs714743	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166732	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv588878	chr22:28248840-28314113	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12160891	SMARCB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28239200-28259400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr22:28240800-28258400	Strong transcription	Thymus	Thymus
3	chr22:28241400-28257800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr22:28241400-28261600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr22:28241600-28258000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr22:28242000-28259400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr22:28242200-28259000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr22:28242200-28259400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr22:28242400-28263200	Strong transcription	GM12878-XiMat	blood
10	chr22:28242600-28258200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr22:28242600-28259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr22:28242600-28259400	Strong transcription	NHEK	skin
13	chr22:28242800-28259400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr22:28243200-28256400	Strong transcription	Primary B cells from cord blood	blood
15	chr22:28243800-28256200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:28243800-28259600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr22:28243800-28274000	Strong transcription	Dnd41	blood
18	chr22:28244000-28261800	Strong transcription	HMEC	breast
19	chr22:28244000-28263600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr22:28244200-28264200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr22:28246400-28259400	Strong transcription	Placenta	Placenta
22	chr22:28246800-28258000	Strong transcription	Fetal Thymus	thymus
23	chr22:28246800-28258200	Strong transcription	NH-A	brain
24	chr22:28246800-28259000	Strong transcription	Fetal Muscle Leg	muscle
25	chr22:28247000-28258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr22:28247000-28311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr22:28247400-28256200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr22:28247400-28256200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr22:28247600-28258000	Strong transcription	HUVEC	blood vessel
30	chr22:28248200-28258000	Strong transcription	HepG2	liver
31	chr22:28248600-28263000	Weak transcription	Right Atrium	heart
32	chr22:28248800-28256800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr22:28248800-28258200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:28249800-28259000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr22:28249800-28261400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr22:28249800-28262200	Weak transcription	Fetal Brain Male	brain
37	chr22:28250000-28259000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:28250000-28259000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:28250200-28256200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr22:28250200-28259000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:28250800-28256400	Strong transcription	Adipose Nuclei	Adipose
42	chr22:28250800-28256600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr22:28250800-28258200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr22:28250800-28259400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr22:28251000-28256600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr22:28251200-28257800	Genic enhancers	Fetal Intestine Large	intestine
47	chr22:28251400-28256200	Strong transcription	Fetal Kidney	kidney
48	chr22:28251600-28256200	Genic enhancers	NHLF	lung
49	chr22:28251600-28259000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:28251600-28267400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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