Variant report

Variant	rs458196
Chromosome Location	chr22:29978026-29978027
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr22:29977881-29978098	T-47D	breast:	n/a	n/a
2	ZNF217	chr22:29977883-29978133	MCF-7	breast:	n/a	n/a
3	GATA3	chr22:29977866-29978145	MCF-7	breast:	n/a	n/a
4	GATA3	chr22:29977838-29978221	MCF-7	breast:	n/a	n/a
5	POLR2A	chr22:29977853-29978060	K562	blood:	n/a	n/a
6	GATA3	chr22:29977643-29978432	MCF-7	breast:	n/a	n/a
7	TCF7L2	chr22:29977874-29978195	MCF-7	breast:	n/a	n/a
8	GATA3	chr22:29977701-29978310	T-47D	breast:	n/a	n/a
9	GATA3	chr22:29977744-29978267	T-47D	breast:	n/a	n/a
10	POLR2A	chr22:29977947-29978049	GM12878	blood:	n/a	n/a
11	HDAC2	chr22:29977806-29978311	MCF-7	breast:	n/a	n/a
12	HDAC2	chr22:29977709-29978255	MCF-7	breast:	n/a	n/a
13	MAX	chr22:29977574-29978173	MCF-7	breast:	n/a	n/a
14	NR2F2	chr22:29977699-29978361	MCF-7	breast:	n/a	n/a
15	GATA3	chr22:29977628-29978470	MCF-7	breast:	n/a	n/a
16	POLR2A	chr22:29977922-29978036	HepG2	liver:	n/a	n/a
17	GABPA	chr22:29977817-29978181	MCF-7	breast:	n/a	n/a
18	POLR2A	chr22:29976318-29978116	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr22:29977604-29978371	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29975483..29978642-chr22:29996311..30000725,6	MCF-7	breast:
2	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:
3	chr22:29663275..29666008-chr22:29976454..29978804,2	K562	blood:
4	chr22:29948374..29951089-chr22:29975785..29978624,4	MCF-7	breast:
5	chr22:29782601..29785697-chr22:29975164..29978533,5	MCF-7	breast:
6	chr22:29975560..29978145-chr22:29998416..30001350,4	MCF-7	breast:
7	chr22:29948193..29950224-chr22:29975940..29978547,6	MCF-7	breast:

No data

Variant related genes	Relation type
NIPSNAP1	TF binding region
ENSG00000182944	Chromatin interaction
ENSG00000100296	Chromatin interaction
ENSG00000100280	Chromatin interaction
ENSG00000186575	Chromatin interaction
ENSG00000100263	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1006396	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10427824	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1049534	0.86[JPT][hapmap]
rs11704899	0.94[CEU][hapmap]
rs11705569	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16987752	1.00[YRI][hapmap]
rs16987832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987839	0.90[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]
rs2247753	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]
rs2262240	0.83[ASN][1000 genomes]
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];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530658	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2530664	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2531848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2531849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs425992	0.88[ASN][1000 genomes]
rs433194	0.86[ASN][1000 genomes]
rs456285	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs456585	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459450	0.87[ASN][1000 genomes]
rs460428	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs460994	0.87[ASN][1000 genomes]
rs462444	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs463220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs465742	0.81[EUR][1000 genomes]
rs468224	0.84[ASN][1000 genomes]
rs468254	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468475	0.86[ASN][1000 genomes]
rs468692	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs468795	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468852	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469230	0.86[ASN][1000 genomes]
rs469253	0.86[ASN][1000 genomes]
rs469295	0.85[ASN][1000 genomes]
rs469363	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs469565	0.85[ASN][1000 genomes]
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];0.83[EUR][1000 genomes]
rs5763306	0.87[JPT][hapmap]
rs5763349	0.89[ASN][1000 genomes]
rs57995869	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs695525	0.89[ASN][1000 genomes]
rs695780	0.86[ASN][1000 genomes]
rs695816	0.89[ASN][1000 genomes]
rs73159040	0.89[ASN][1000 genomes]
rs7609	0.92[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8135828	0.94[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8141518	0.89[ASN][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	nsv521852	chr22:29974831-29983138	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs458196	THOC5	cis	Adipose Subcutaneous	GTEx
rs458196	THOC5	cis	Artery Tibial	GTEx
rs458196	THOC5	cis	Muscle Skeletal	GTEx
rs458196	NIPSNAP1	cis	Stomach	GTEx
rs458196	THOC5	cis	Nerve Tibial	GTEx
rs458196	THOC5	cis	lung	GTEx
rs458196	THOC5	cis	Esophagus Muscularis	GTEx
rs458196	THOC5	cis	Artery Aorta	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29976800-29978200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr22:29977200-29978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:29977200-29978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29977400-29978200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:29977400-29978200	Enhancers	HMEC	breast
6	chr22:29977600-29978200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:29977600-29978200	Flanking Active TSS	Dnd41	blood
8	chr22:29977600-29978200	Flanking Active TSS	NHEK	skin
9	chr22:29977600-29979200	Enhancers	Thymus	Thymus
10	chr22:29977600-29998800	Weak transcription	Right Atrium	heart
11	chr22:29977800-29978200	Enhancers	Primary B cells from peripheral blood	blood
12	chr22:29977800-29978200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr22:29977800-29978200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr22:29977800-29978200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr22:29977800-29978200	Enhancers	Hela-S3	cervix
16	chr22:29977800-29978600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr22:29977800-29978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:29977800-29979000	Enhancers	Placenta	Placenta
19	chr22:29977800-29979200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr22:29977800-29979400	Enhancers	Fetal Thymus	thymus
21	chr22:29977800-29979400	Enhancers	HepG2	liver
22	chr22:29977800-29984000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:29977800-29994200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr22:29978000-29978200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr22:29978000-29978200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:29978000-29978200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:29978000-29978200	Active TSS	Duodenum Mucosa	Duodenum
28	chr22:29978000-29978200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr22:29978000-29979000	Enhancers	K562	blood
30	chr22:29978000-29979200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr22:29978000-29983200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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