Variant report

Variant	rs7289941
Chromosome Location	chr22:31884405-31884406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr22:31884307-31884694	GM12878	blood:	n/a	chr22:31884501-31884511 chr22:31884504-31884515
2	POLR2A	chr22:31884391-31888525	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31884354..31887535-chr22:32340375..32343416,3	MCF-7	breast:
2	chr14:60714772..60717731-chr22:31883101..31885338,2	MCF-7	breast:
3	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
4	chr22:31883675..31887496-chr22:32025240..32029301,5	K562	blood:
5	22:31864703-31891033..22:31930706-31935473	GM12878	blood:
6	22:31864703-31891033..22:32347255-32351014	K562	blood:
7	chr22:31850201..31852811-chr22:31884349..31886700,2	MCF-7	breast:
8	chr22:31742290..31744009-chr22:31883766..31886602,4	MCF-7	breast:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000254718	Chromatin interaction
ENSG00000100614	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000238910	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000240591	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000128254	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11704494	0.93[EUR][1000 genomes]
rs1916	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap]
rs2006771	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs2012451	0.81[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs35143518	0.86[EUR][1000 genomes]
rs4541328	0.96[EUR][1000 genomes]
rs4820048	0.85[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4820974	0.89[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4820978	0.80[AFR][1000 genomes]
rs4820983	0.83[YRI][hapmap]
rs55694512	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749302	0.84[EUR][1000 genomes]
rs5753667	0.87[LWK][hapmap];0.80[YRI][hapmap]
rs5997971	0.82[YRI][hapmap]
rs5997988	0.85[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs5997989	0.87[EUR][1000 genomes]
rs5998002	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs5998003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998004	0.98[EUR][1000 genomes]
rs5998012	0.96[EUR][1000 genomes]
rs5998016	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5998017	0.95[EUR][1000 genomes]
rs5998021	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6518752	0.91[CHB][hapmap];0.83[CHD][hapmap];0.92[MEX][hapmap]
rs7287937	1.00[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs8140312	0.91[CHB][hapmap];0.88[MEX][hapmap]
rs8142376	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7289941	MN1	cis	parietal	SCAN
rs7289941	CRYBB1	cis	cerebellum	SCAN
rs7289941	SELM	cis	parietal	SCAN
rs7289941	NF2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:31854800-31884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31856800-31885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:31858400-31884600	Weak transcription	Psoas Muscle	Psoas
5	chr22:31859400-31884800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:31860200-31884800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:31864400-31884600	Weak transcription	Aorta	Aorta
8	chr22:31864600-31884600	Weak transcription	Right Ventricle	heart
9	chr22:31867600-31884600	Weak transcription	Pancreas	Pancrea
10	chr22:31874400-31884600	Weak transcription	Stomach Mucosa	stomach
11	chr22:31875800-31884600	Weak transcription	Colonic Mucosa	Colon
12	chr22:31878000-31884600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:31878000-31885000	Weak transcription	Esophagus	oesophagus
14	chr22:31878400-31884600	Weak transcription	Small Intestine	intestine
15	chr22:31878400-31884600	Weak transcription	Spleen	Spleen
16	chr22:31879800-31884600	Weak transcription	Thymus	Thymus
17	chr22:31880000-31884600	Weak transcription	Fetal Brain Male	brain
18	chr22:31880400-31884600	Weak transcription	HSMMtube	muscle
19	chr22:31881600-31884600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:31881800-31885000	Weak transcription	Gastric	stomach
21	chr22:31882800-31885000	Weak transcription	Left Ventricle	heart
22	chr22:31883000-31884600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr22:31883000-31884600	Genic enhancers	Fetal Heart	heart
24	chr22:31883200-31884600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr22:31883200-31884600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:31883200-31884800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr22:31883400-31884600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr22:31883400-31884600	Genic enhancers	Colon Smooth Muscle	Colon
29	chr22:31883400-31884600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr22:31883600-31884600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:31883600-31884600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr22:31883600-31884600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr22:31883600-31884600	Genic enhancers	Brain Hippocampus Middle	brain
34	chr22:31883600-31884800	Weak transcription	Ovary	ovary
35	chr22:31883800-31884600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:31883800-31884600	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr22:31883800-31884600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr22:31883800-31884600	Genic enhancers	Liver	Liver
39	chr22:31883800-31885000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr22:31883800-31885000	Weak transcription	Lung	lung
41	chr22:31884000-31884600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr22:31884000-31884600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr22:31884000-31884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr22:31884000-31884600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr22:31884000-31884600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr22:31884000-31884600	Enhancers	Brain Cingulate Gyrus	brain
47	chr22:31884000-31884800	Flanking Active TSS	HMEC	breast
48	chr22:31884000-31885000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr22:31884200-31884600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr22:31884200-31884600	Enhancers	Primary monocytes fromperipheralblood	blood

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