Variant report

Variant	rs1355620
Chromosome Location	chr9:98270168-98270169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:98267921-98270672	HUVEC	blood vessel:	n/a	n/a
2	MXI1	chr9:98267312-98274672	IMR90	lung:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
3	ELF1	chr9:98269994-98270406	A549	lung:	n/a	n/a
4	POLR2A	chr9:98267977-98272043	Hela-S3	cervix:	n/a	n/a
5	TEAD4	chr9:98269286-98270577	ECC-1	luminal epithelium:	n/a	n/a
6	TAF1	chr9:98270079-98270516	PFSK-1	brain:	n/a	n/a
7	UBTF	chr9:98267992-98271724	K562	blood:	n/a	n/a
8	FOSL2	chr9:98269618-98270577	A549	lung:	n/a	chr9:98269836-98269850
9	POLR2A	chr9:98269890-98270652	ECC-1	luminal epithelium:	n/a	n/a
10	TBP	chr9:98269125-98270595	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr9:98267962-98271933	GM12892	blood:	n/a	n/a
12	CHD1	chr9:98269359-98270459	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYBL2	chr9:98270092-98270496	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:98270117-98270551	SK-N-SH	brain:	n/a	n/a
15	EBF1	chr9:98267827-98270460	GM12878	blood:	n/a	chr9:98268878-98268889
16	FOXA2	chr9:98269512-98270531	A549	lung:	n/a	n/a
17	SIN3A	chr9:98266518-98275316	H1-hESC	embryonic stem cell:	n/a	chr9:98268478-98268491 chr9:98273259-98273270 chr9:98273104-98273113 chr9:98271212-98271225 chr9:98270756-98270767 chr9:98271270-98271279 chr9:98272257-98272268 chr9:98273102-98273111 chr9:98271251-98271264
18	CEBPD	chr9:98269834-98270200	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr9:98270059-98270375	HepG2	liver:	n/a	n/a
20	POLR2A	chr9:98270127-98270191	MCF-7	breast:	n/a	n/a
21	SIN3AK20	chr9:98269890-98270495	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr9:98268067-98270930	Hela-S3	cervix:	n/a	n/a
23	SIN3AK20	chr9:98269151-98270682	HCT-116	colon:	n/a	n/a
24	EP300	chr9:98269206-98270588	A549	lung:	n/a	chr9:98269627-98269643 chr9:98269628-98269644 chr9:98270408-98270422 chr9:98269417-98269426
25	MAZ	chr9:98267922-98270765	Hela-S3	cervix:	n/a	chr9:98269402-98269412 chr9:98268933-98268942
26	CTCF	chr9:98270100-98270250	HCPEpiC	choroid plexus:	n/a	n/a
27	MYC	chr9:98267952-98270353	NB4	blood:	n/a	chr9:98269402-98269412 chr9:98268933-98268942
28	ZBTB7A	chr9:98269955-98270235	HepG2	liver:	n/a	n/a
29	HMGN3	chr9:98269995-98271950	K562	blood:	n/a	n/a
30	SMARCB1	chr9:98268002-98271392	Hela-S3	cervix:	n/a	n/a
31	MYC	chr9:98270144-98270389	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr9:98268168-98270457	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr9:98267858-98270619	K562	blood:	n/a	n/a
34	SIN3AK20	chr9:98269380-98270569	A549	lung:	n/a	n/a
35	POLR2A	chr9:98267935-98270910	GM15510	blood:	n/a	n/a
36	TAF1	chr9:98270168-98270469	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr9:98270035-98270168	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:98267866-98270464	GM12878	blood:	n/a	n/a
39	POLR2A	chr9:98268890-98270576	SK-N-MC	brain:	n/a	n/a
40	GATA3	chr9:98269404-98270646	SK-N-SH	brain:	n/a	n/a
41	GABPA	chr9:98270032-98270383	K562	blood:	n/a	n/a
42	TCF12	chr9:98268998-98270496	SK-N-SH	brain:	n/a	chr9:98269495-98269502
43	RUNX3	chr9:98267855-98270599	GM12878	blood:	n/a	n/a
44	POLR2A	chr9:98267946-98270837	GM19099	blood:	n/a	n/a
45	STAT3	chr9:98269787-98270359	MCF10A-Er-Src	breast:	n/a	chr9:98269929-98269940 chr9:98269865-98269888
46	STAT1	chr9:98270056-98270250	GM12878	blood:	n/a	n/a
47	YY1	chr9:98270130-98270466	A549	lung:	n/a	n/a
48	POLR2A	chr9:98268225-98270371	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr9:98270163-98270519	HCT-116	colon:	n/a	n/a
50	ATF2	chr9:98269704-98270383	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
2	chr9:98187696..98190762-chr9:98268567..98271378,5	MCF-7	breast:
3	chr9:98078830..98081414-chr9:98266391..98270806,3	MCF-7	breast:
4	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
5	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
6	chr9:98186276..98191956-chr9:98269234..98276633,9	K562	blood:
7	chr9:98078123..98080907-chr9:98268002..98270715,3	K562	blood:
8	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
9	chr9:98254778..98257186-chr9:98269292..98272061,2	MCF-7	breast:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000158169	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10512248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355619	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066829	0.83[ASN][1000 genomes]
rs2236407	0.83[ASN][1000 genomes]
rs2282042	0.84[ASN][1000 genomes]
rs2297086	0.83[ASN][1000 genomes]
rs2297088	0.83[ASN][1000 genomes]
rs28457763	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495472	0.83[ASN][1000 genomes]
rs28496034	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28504650	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28536201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557305	0.84[ASN][1000 genomes]
rs28591501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28620668	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758302	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3327711	chr9:98266981-98273279	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3396612	chr9:98269556-98272304	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98265800-98271600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr9:98266400-98271600	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr9:98266600-98275000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:98267000-98270400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr9:98267000-98274800	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr9:98267200-98273600	Active TSS	Right Atrium	heart
7	chr9:98267200-98274000	Active TSS	Fetal Intestine Large	intestine
8	chr9:98267200-98274200	Active TSS	Left Ventricle	heart
9	chr9:98267200-98274400	Active TSS	Ovary	ovary
10	chr9:98267400-98272000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:98267400-98273800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:98267400-98273800	Active TSS	Fetal Intestine Small	intestine
13	chr9:98267400-98273800	Active TSS	Fetal Kidney	kidney
14	chr9:98267400-98273800	Active TSS	Small Intestine	intestine
15	chr9:98267400-98274000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr9:98267400-98274400	Active TSS	NHDF-Ad	bronchial
17	chr9:98267400-98274600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:98267400-98274800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:98267600-98271800	Active TSS	GM12878-XiMat	blood
20	chr9:98267600-98274000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr9:98267600-98274000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:98267600-98274000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:98267600-98274000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:98267600-98274000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:98267600-98274000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:98267600-98274000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:98267600-98274000	Active TSS	Psoas Muscle	Psoas
28	chr9:98267600-98274200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:98267600-98274400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:98267600-98274400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:98267600-98274600	Active TSS	NHLF	lung
32	chr9:98267600-98274800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:98267800-98270400	Bivalent/Poised TSS	HepG2	liver
34	chr9:98267800-98270600	Active TSS	Fetal Heart	heart
35	chr9:98267800-98271600	Active TSS	Hela-S3	cervix
36	chr9:98267800-98271800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr9:98267800-98272200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:98267800-98273600	Active TSS	Lung	lung
39	chr9:98267800-98273800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:98267800-98273800	Active TSS	Duodenum Mucosa	Duodenum
41	chr9:98267800-98273800	Active TSS	HSMMtube	muscle
42	chr9:98267800-98274000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:98267800-98274000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:98267800-98274000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr9:98267800-98274000	Active TSS	A549	lung
46	chr9:98267800-98274200	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr9:98267800-98274200	Active TSS	Aorta	Aorta
48	chr9:98267800-98274200	Active TSS	Brain Cingulate Gyrus	brain
49	chr9:98267800-98274200	Active TSS	Brain Hippocampus Middle	brain
50	chr9:98267800-98274200	Active TSS	Brain Substantia Nigra	brain

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