Variant report

Variant	rs10500842
Chromosome Location	chr11:19164862-19164863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:19162993..19165619-chr11:19174765..19176365,2	K562	blood:
2	chr11:19164352..19166068-chr11:19175004..19177125,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10500841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs10741761	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10766528	1.00[ASN][1000 genomes]
rs10833064	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10833065	1.00[ASN][1000 genomes]
rs11025021	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11025025	0.99[ASN][1000 genomes]
rs11025026	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11025037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs11607797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12270581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs1393954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393955	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1503507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1875724	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2042688	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2134622	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2271001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28891775	0.90[ASN][1000 genomes]
rs3758875	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3802797	0.97[ASN][1000 genomes]
rs4326774	0.85[ASN][1000 genomes]
rs4757757	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4757758	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs4757759	1.00[ASN][1000 genomes]
rs4757760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs59393175	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103110	0.97[ASN][1000 genomes]
rs7111105	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7111919	0.91[AMR][1000 genomes]
rs7120462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7129212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7129326	1.00[ASN][1000 genomes]
rs7934179	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7950603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7950788	1.00[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	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10500842	IGSF22	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19139600-19175000	Weak transcription	Pancreas	Pancrea
2	chr11:19139800-19172000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:19140000-19167600	Weak transcription	HMEC	breast
4	chr11:19140000-19169600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr11:19140000-19186400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:19140200-19175000	Weak transcription	Thymus	Thymus
7	chr11:19140800-19186800	Weak transcription	Colonic Mucosa	Colon
8	chr11:19142000-19168400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:19142800-19173200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:19143200-19167800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:19143400-19185800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:19143400-19186400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:19143400-19201600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:19143600-19167600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:19143600-19170400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:19143600-19197400	Weak transcription	Small Intestine	intestine
17	chr11:19143800-19168600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:19147400-19170600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:19147600-19174200	Weak transcription	Osteobl	bone
20	chr11:19148400-19167400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:19152800-19175000	Weak transcription	Psoas Muscle	Psoas
22	chr11:19153200-19186600	Weak transcription	Aorta	Aorta
23	chr11:19154000-19175000	Weak transcription	Ovary	ovary
24	chr11:19154200-19166800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:19154200-19168400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:19154400-19165200	Weak transcription	HUVEC	blood vessel
27	chr11:19154400-19168800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:19154400-19174800	Weak transcription	Left Ventricle	heart
29	chr11:19154600-19167200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:19154600-19167600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:19154800-19167400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:19154800-19168600	Weak transcription	Primary B cells from cord blood	blood
33	chr11:19154800-19171400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:19154800-19177200	Weak transcription	NHEK	skin
35	chr11:19155400-19170600	Weak transcription	GM12878-XiMat	blood
36	chr11:19156000-19167600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr11:19156000-19168600	Weak transcription	A549	lung
38	chr11:19156200-19167800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr11:19156400-19175400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:19156600-19167200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:19156600-19168400	Weak transcription	Dnd41	blood
42	chr11:19156600-19193200	Weak transcription	Fetal Stomach	stomach
43	chr11:19156800-19167000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:19156800-19167800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:19156800-19167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:19156800-19193800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:19156800-19194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:19157000-19170400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:19157200-19169400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr11:19157200-19186200	Weak transcription	H9 Cell Line	embryonic stem cell

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