Variant report

Variant	rs740219
Chromosome Location	chr22:30714684-30714685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30699910..30702358-chr22:30713888..30716292,3	MCF-7	breast:
2	chr22:30712771..30715254-chr22:30752580..30754854,2	MCF-7	breast:
3	chr22:30713647..30715553-chr22:30779005..30781770,2	MCF-7	breast:
4	chr22:30710430..30716803-chr22:30717996..30724228,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099995	Chromatin interaction
ENSG00000187860	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000099999	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10376	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046199	0.80[CHD][hapmap]
rs2041199	0.89[AMR][1000 genomes]
rs2108093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299830	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4339043	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820844	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4823085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749066	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5753071	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753080	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753088	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753111	1.00[ASN][1000 genomes]
rs5763923	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs737950	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757869	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs929454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv3593	chr22:30705980-30751122	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740219	SELM	cis	parietal	SCAN
rs740219	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
2	chr22:30699600-30715600	Weak transcription	Fetal Brain Female	brain
3	chr22:30702800-30714800	Enhancers	Spleen	Spleen
4	chr22:30705000-30720400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:30706000-30719400	Genic enhancers	Dnd41	blood
6	chr22:30706200-30720000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr22:30706400-30715400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr22:30706400-30716600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr22:30706600-30720400	Genic enhancers	Fetal Thymus	thymus
10	chr22:30707000-30715400	Weak transcription	Brain Germinal Matrix	brain
11	chr22:30707000-30715800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30707400-30715000	Enhancers	Adipose Nuclei	Adipose
13	chr22:30707400-30720800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr22:30707800-30720400	Weak transcription	Fetal Lung	lung
15	chr22:30707800-30720800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr22:30708400-30716800	Weak transcription	Psoas Muscle	Psoas
17	chr22:30708600-30715000	Weak transcription	Fetal Heart	heart
18	chr22:30708800-30715400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr22:30708800-30716200	Weak transcription	HSMMtube	muscle
20	chr22:30709000-30717600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr22:30709200-30715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr22:30709200-30717400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr22:30709400-30714800	Weak transcription	Fetal Muscle Leg	muscle
24	chr22:30709400-30715200	Genic enhancers	Primary T cells from cord blood	blood
25	chr22:30709600-30720600	Strong transcription	Fetal Stomach	stomach
26	chr22:30710000-30717400	Weak transcription	Brain Anterior Caudate	brain
27	chr22:30710200-30715000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr22:30710200-30716400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:30710200-30719800	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr22:30710400-30715600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr22:30710400-30716200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr22:30710400-30720800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr22:30710400-30720800	Weak transcription	Fetal Kidney	kidney
34	chr22:30710600-30720400	Weak transcription	Brain Hippocampus Middle	brain
35	chr22:30710800-30718000	Enhancers	Ovary	ovary
36	chr22:30710800-30718400	Strong transcription	Fetal Intestine Small	intestine
37	chr22:30711000-30717800	Weak transcription	Brain Angular Gyrus	brain
38	chr22:30711200-30715400	Weak transcription	Brain Substantia Nigra	brain
39	chr22:30711200-30716000	Weak transcription	Fetal Intestine Large	intestine
40	chr22:30711200-30720200	Weak transcription	Small Intestine	intestine
41	chr22:30711400-30715800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr22:30711400-30719400	Weak transcription	NH-A	brain
43	chr22:30711800-30715600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr22:30711800-30717000	Weak transcription	K562	blood
45	chr22:30711800-30721200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr22:30712000-30715000	Enhancers	Placenta	Placenta
47	chr22:30712000-30715400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr22:30712000-30715800	Weak transcription	HMEC	breast
49	chr22:30712000-30716200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr22:30712000-30716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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