Variant report

Variant	rs10376
Chromosome Location	chr22:30728356-30728357
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30723090..30724854-chr22:30725952..30728416,2	K562	blood:
2	chr22:30726026..30729085-chr22:30749869..30754191,5	MCF-7	breast:
3	chr22:30679226..30682000-chr22:30723679..30728534,4	K562	blood:
4	chr22:30721780..30724167-chr22:30728041..30729954,3	MCF-7	breast:
5	chr22:30728274..30730328-chr22:30731097..30733421,3	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10427610	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041199	0.89[AMR][1000 genomes]
rs2108093	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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299830	0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs4339043	1.00[ASW][hapmap];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820831	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.88[ASN][1000 genomes]
rs4820844	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs4823085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749082	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5753071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753080	1.00[ASW][hapmap];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753088	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753111	1.00[ASN][1000 genomes]
rs5763923	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs737950	1.00[ASW][hapmap];1.00[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740219	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]
rs757869	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs929454	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608904	0.92[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620966	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1064350	chr22:30724148-30742125	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	n/a
8	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10376	SF3A1	cis	multi-tissue	Pritchard
rs10376	SELM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30723000-30728400	Weak transcription	Small Intestine	intestine
2	chr22:30723400-30728400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30723400-30728600	Weak transcription	Esophagus	oesophagus
4	chr22:30723400-30728600	Weak transcription	Right Ventricle	heart
5	chr22:30723400-30728800	Weak transcription	Ovary	ovary
6	chr22:30723400-30729400	Weak transcription	Psoas Muscle	Psoas
7	chr22:30723400-30732600	Weak transcription	Right Atrium	heart
8	chr22:30723600-30728400	Weak transcription	Brain Hippocampus Middle	brain
9	chr22:30723600-30728400	Weak transcription	Colon Smooth Muscle	Colon
10	chr22:30723600-30728600	Weak transcription	Aorta	Aorta
11	chr22:30723600-30729400	Weak transcription	Fetal Brain Male	brain
12	chr22:30723600-30730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:30723600-30751600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:30723800-30728400	Weak transcription	Brain Angular Gyrus	brain
15	chr22:30723800-30729200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr22:30723800-30742800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr22:30724000-30728600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr22:30724000-30728600	Weak transcription	Pancreas	Pancrea
19	chr22:30724000-30729200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:30724200-30728400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr22:30724200-30728400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr22:30724200-30728400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr22:30724200-30731200	Weak transcription	Hela-S3	cervix
24	chr22:30724400-30728400	Weak transcription	HMEC	breast
25	chr22:30724400-30729200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr22:30724400-30750000	Strong transcription	Thymus	Thymus
27	chr22:30724600-30728400	Weak transcription	HepG2	liver
28	chr22:30724600-30729400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:30724600-30750200	Strong transcription	Osteobl	bone
30	chr22:30724800-30728600	Weak transcription	Stomach Mucosa	stomach
31	chr22:30724800-30745200	Strong transcription	NHEK	skin
32	chr22:30724800-30750200	Strong transcription	Fetal Intestine Small	intestine
33	chr22:30725000-30729400	Weak transcription	Fetal Heart	heart
34	chr22:30725200-30733200	Strong transcription	Fetal Muscle Leg	muscle
35	chr22:30725400-30733400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr22:30725400-30743400	Strong transcription	Fetal Stomach	stomach
37	chr22:30725400-30749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr22:30725400-30750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:30725600-30729400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr22:30725600-30733600	Genic enhancers	Placenta	Placenta
41	chr22:30725600-30743600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:30725600-30744200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr22:30725600-30750200	Strong transcription	Fetal Intestine Large	intestine
44	chr22:30725800-30728800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr22:30725800-30732400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:30725800-30732800	Strong transcription	Liver	Liver
47	chr22:30725800-30736800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:30725800-30740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr22:30725800-30742600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr22:30725800-30743200	Strong transcription	Fetal Thymus	thymus

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