Variant report

Variant	rs2247753
Chromosome Location	chr22:30022936-30022937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30013839..30015515-chr22:30021150..30023734,2	MCF-7	breast:
2	chr22:30021415..30023125-chr22:30030680..30033150,2	K562	blood:
3	chr22:30002723..30005398-chr22:30022131..30024031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233010	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1006396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10427824	0.91[AFR][1000 genomes]
rs1049534	0.86[JPT][hapmap]
rs11704899	0.94[CEU][hapmap]
rs11705569	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs16987752	1.00[YRI][hapmap]
rs16987832	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072303	1.00[YRI][hapmap]
rs2074947	1.00[YRI][hapmap]
rs2074948	0.86[JPT][hapmap]
rs2074949	1.00[YRI][hapmap]
rs2074950	1.00[YRI][hapmap]
rs2267146	1.00[YRI][hapmap]
rs2267152	0.88[CEU][hapmap]
rs2270079	1.00[YRI][hapmap]
rs2302140	1.00[YRI][hapmap]
rs2302141	0.86[JPT][hapmap]
rs2302142	1.00[YRI][hapmap]
rs2527336	0.87[CEU][hapmap]
rs2530656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2530658	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2530664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531849	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs456285	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs456585	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs458196	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs460428	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs462444	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs463220	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468254	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs468692	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs468795	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs468852	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs469363	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs5763297	0.86[JPT][hapmap]
rs5763301	0.86[JPT][hapmap]
rs5763303	0.87[JPT][hapmap]
rs5763305	0.94[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs5763306	0.87[JPT][hapmap]
rs57995869	0.91[AFR][1000 genomes]
rs7609	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs8135828	0.94[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2247753	NIPSNAP1	cis	Stomach	GTEx
rs2247753	THOC5	cis	Nerve Tibial	GTEx
rs2247753	THOC5	cis	Adipose Subcutaneous	GTEx
rs2247753	THOC5	cis	Artery Aorta	GTEx
rs2247753	THOC5	cis	Muscle Skeletal	GTEx
rs2247753	THOC5	cis	Artery Tibial	GTEx
rs2247753	THOC5	cis	lung	GTEx
rs2247753	THOC5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
4	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30014800-30032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:30015400-30026400	Weak transcription	Brain Anterior Caudate	brain
7	chr22:30016000-30023200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:30018000-30026400	Weak transcription	Right Atrium	heart
9	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:30018200-30023000	Enhancers	Hela-S3	cervix
11	chr22:30018200-30023200	Enhancers	HSMM	muscle
12	chr22:30018200-30024400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:30018200-30024600	Enhancers	HMEC	breast
14	chr22:30018400-30023800	Enhancers	HSMMtube	muscle
15	chr22:30018400-30025000	Weak transcription	Fetal Intestine Small	intestine
16	chr22:30018400-30025800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr22:30018600-30023800	Enhancers	HUVEC	blood vessel
19	chr22:30018600-30024400	Enhancers	NHLF	lung
20	chr22:30018800-30024400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr22:30019000-30023600	Enhancers	A549	lung
22	chr22:30019000-30024400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr22:30019600-30026800	Enhancers	Dnd41	blood
24	chr22:30019600-30029400	Weak transcription	Esophagus	oesophagus
25	chr22:30019800-30023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr22:30019800-30023000	Enhancers	NHEK	skin
27	chr22:30019800-30033800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr22:30020000-30024400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr22:30020000-30026400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:30020200-30029400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr22:30020200-30033200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr22:30020200-30033600	Weak transcription	GM12878-XiMat	blood
33	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
34	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
35	chr22:30020400-30032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr22:30020400-30033400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:30020600-30023800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr22:30020600-30026400	Weak transcription	Right Ventricle	heart
39	chr22:30020600-30028200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr22:30020600-30029200	Weak transcription	Thymus	Thymus
41	chr22:30020600-30032800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr22:30020800-30029200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
44	chr22:30021200-30023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr22:30021200-30026400	Weak transcription	Left Ventricle	heart
46	chr22:30021200-30026400	Weak transcription	Spleen	Spleen
47	chr22:30021200-30026600	Weak transcription	Lung	lung
48	chr22:30021200-30029400	Weak transcription	Fetal Muscle Leg	muscle
49	chr22:30021200-30033200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr22:30021400-30023200	Enhancers	HepG2	liver

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