Variant report

Variant	rs1009147
Chromosome Location	chr22:30088257-30088258
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	chr22:30086550..30091376-chr22:30091742..30099600,10	MCF-7	breast:
2	chr22:30086357..30088684-chr22:30160929..30163029,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008515	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11090576	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16987914	0.83[AFR][1000 genomes]
rs17460259	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17462054	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800540	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1970776	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2008880	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs2079339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079648	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2530678	0.90[LWK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs2530680	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2857629	0.94[AFR][1000 genomes]
rs2857634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs457930	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs467669	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs467768	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs4823046	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs4823048	0.83[EUR][1000 genomes]
rs5763315	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs5763347	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5763348	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5997506	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6006219	1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6006225	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737979	1.00[JPT][hapmap]
rs8135737	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv914965	chr22:30086144-30112226	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1009147	SGSM1	cis	cerebellum	SCAN
rs1009147	NEFH	cis	multi-tissue	Pritchard
rs1009147	CABIN1	cis	parietal	SCAN
rs1009147	SEC14L4	cis	cerebellum	SCAN
rs1009147	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
2	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
5	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr22:30060200-30093600	Strong transcription	Fetal Thymus	thymus
7	chr22:30063400-30094600	Strong transcription	Primary T cells from cord blood	blood
8	chr22:30075400-30097400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr22:30076800-30096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr22:30077800-30096400	Weak transcription	Small Intestine	intestine
11	chr22:30079600-30097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:30079600-30097400	Weak transcription	Hela-S3	cervix
13	chr22:30080000-30097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr22:30080200-30089600	Weak transcription	Colonic Mucosa	Colon
15	chr22:30080200-30098800	Weak transcription	GM12878-XiMat	blood
16	chr22:30081000-30096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr22:30081200-30096400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr22:30081400-30089000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:30082000-30088800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr22:30083200-30090000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr22:30083400-30089000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:30083800-30088400	Weak transcription	Primary B cells from cord blood	blood
23	chr22:30083800-30088400	Weak transcription	Fetal Intestine Large	intestine
24	chr22:30084000-30089400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr22:30084000-30090000	Weak transcription	Aorta	Aorta
26	chr22:30084200-30088800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr22:30084400-30088600	Weak transcription	Left Ventricle	heart
28	chr22:30084400-30089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr22:30084400-30089000	Weak transcription	HUVEC	blood vessel
30	chr22:30084400-30089600	Weak transcription	HMEC	breast
31	chr22:30084400-30090400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr22:30084600-30088600	Weak transcription	Gastric	stomach
33	chr22:30084600-30089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:30084600-30089800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr22:30085000-30089000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr22:30085200-30088400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr22:30085200-30088400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr22:30085200-30088400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr22:30085200-30088800	Strong transcription	NHEK	skin
40	chr22:30085600-30088400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr22:30085600-30092000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr22:30085600-30094000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr22:30085800-30089000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:30085800-30089200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr22:30085800-30089200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:30085800-30095000	Strong transcription	Dnd41	blood
47	chr22:30085800-30096200	Weak transcription	Fetal Kidney	kidney
48	chr22:30086000-30089800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr22:30086000-30090000	Weak transcription	Fetal Lung	lung
50	chr22:30086000-30090000	Weak transcription	Osteobl	bone

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