Variant report

Variant	rs3758302
Chromosome Location	chr9:98272630-98272631
allele	C/G
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	chr9:98272611-98274009	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr9:98267312-98274672	IMR90	lung:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
3	MXI1	chr9:98272581-98274289	GM12878	blood:	n/a	chr9:98273104-98273113
4	MAX	chr9:98272488-98274201	A549	lung:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
5	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
6	POLR2A	chr9:98272627-98273993	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr9:98272617-98272824	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:98272527-98274020	PFSK-1	brain:	n/a	n/a
9	MAX	chr9:98272558-98272777	K562	blood:	n/a	n/a
10	POLR2A	chr9:98272119-98274533	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr9:98268396-98274155	H1-neurons	neurons:	n/a	n/a
12	MTA3	chr9:98272456-98273381	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:98272558-98272696	HepG2	liver:	n/a	n/a
14	MAX	chr9:98272511-98274616	Hela-S3	cervix:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
15	POLR2A	chr9:98271093-98274127	H1-neurons	neurons:	n/a	n/a
16	TEAD4	chr9:98272620-98274052	K562	blood:	n/a	chr9:98272812-98272821
17	TCF12	chr9:98271325-98273457	A549	lung:	n/a	chr9:98271659-98271668
18	E2F4	chr9:98272323-98274375	MCF10A-Er-Src	breast:	n/a	chr9:98273817-98273826 chr9:98273343-98273352 chr9:98273266-98273275
19	REST	chr9:98267183-98274539	H1-neurons	neurons:	n/a	chr9:98270976-98270989 chr9:98268273-98268286 chr9:98271222-98271240 chr9:98270100-98270109 chr9:98270699-98270717 chr9:98271458-98271466 chr9:98268565-98268575 chr9:98271242-98271255 chr9:98269758-98269778
20	USF1	chr9:98272619-98274154	SK-N-SH	brain:	n/a	chr9:98273204-98273220 chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
21	TBP	chr9:98272467-98273204	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr9:98272598-98274391	IMR90	lung:	n/a	n/a
23	ARID3A	chr9:98272431-98273341	HepG2	liver:	n/a	n/a
24	MAX	chr9:98272505-98274336	HCT-116	colon:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
25	ZNF384	chr9:98271304-98273242	K562	blood:	n/a	n/a
26	POLR2A	chr9:98272579-98273998	Raji	blood:	n/a	n/a
27	POLR2A	chr9:98272435-98275174	SK-N-MC	brain:	n/a	n/a
28	RFX5	chr9:98272512-98274108	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr9:98272563-98273164	H1-neurons	neurons:	n/a	n/a
30	MYC	chr9:98272581-98275186	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
31	MAX	chr9:98272564-98274705	HepG2	liver:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
32	MYC	chr9:98272592-98275333	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
33	YY1	chr9:98272597-98272770	K562	blood:	n/a	n/a
34	MAX	chr9:98272579-98272665	HepG2	liver:	n/a	n/a
35	HA-E2F1	chr9:98272591-98274205	MCF-7	breast:	n/a	chr9:98273817-98273826 chr9:98273343-98273352 chr9:98273266-98273275
36	RFX5	chr9:98271125-98274717	SK-N-SH	brain:	n/a	chr9:98271680-98271694 chr9:98271679-98271695 chr9:98274209-98274223 chr9:98271682-98271696 chr9:98271681-98271696
37	MAX	chr9:98272560-98273243	SK-N-SH	brain:	n/a	chr9:98273103-98273112 chr9:98273101-98273114 chr9:98273102-98273113 chr9:98273101-98273114 chr9:98273103-98273112
38	MAZ	chr9:98272199-98274575	IMR90	lung:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
39	SIN3AK20	chr9:98272560-98273441	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr9:98271292-98278496	K562	blood:	n/a	n/a
41	RAD21	chr9:98272582-98273319	IMR90	lung:	n/a	n/a
42	POLR2A	chr9:98272530-98274031	K562	blood:	n/a	n/a
43	CHD2	chr9:98272608-98272785	K562	blood:	n/a	n/a
44	MYC	chr9:98271570-98274593	MCF10A-Er-Src	breast:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
45	MXI1	chr9:98267369-98275571	SK-N-SH	brain:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
46	CHD2	chr9:98272554-98273996	Hela-S3	cervix:	n/a	n/a
47	TAF1	chr9:98272620-98273449	H1-neurons	neurons:	n/a	n/a
48	BACH1	chr9:98272441-98273859	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr9:98272611-98273340	ECC-1	luminal epithelium:	n/a	chr9:98273103-98273112 chr9:98273101-98273114 chr9:98273102-98273113 chr9:98273101-98273114 chr9:98273103-98273112
50	CHD1	chr9:98272391-98273040	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98272232..98274861-chr9:98331837..98334312,2	MCF-7	breast:
2	chr9:98271476..98273669-chr9:98979149..98980872,2	MCF-7	breast:
3	chr9:98253127..98255795-chr9:98271024..98273748,2	K562	blood:
4	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
5	chr9:98079077..98082863-chr9:98272048..98274634,4	MCF-7	breast:
6	chr9:98256366..98258410-chr9:98271924..98274612,2	K562	blood:
7	chr9:98218003..98222058-chr9:98271885..98274474,3	K562	blood:
8	chr9:98271289..98274209-chr9:98357697..98360375,2	MCF-7	breast:
9	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
10	chr9:98184245..98186249-chr9:98271181..98273183,2	K562	blood:
11	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
12	chr9:98186276..98191956-chr9:98269234..98276633,9	K562	blood:
13	chr9:98192901..98194795-chr9:98272389..98274432,2	K562	blood:
14	chr9:98268284..98270797-chr9:98272240..98274371,3	MCF-7	breast:
15	chr9:98078136..98081236-chr9:98271605..98275803,7	K562	blood:
16	chr9:98143874..98147656-chr9:98271045..98275159,6	MCF-7	breast:
17	chr9:98227014..98229023-chr9:98271434..98274318,2	MCF-7	breast:
18	chr9:98270649..98275167-chr9:98636318..98639773,5	MCF-7	breast:
19	chr9:98010532..98014660-chr9:98272495..98275814,3	K562	blood:
20	chr9:98187721..98190114-chr9:98271481..98273732,2	MCF-7	breast:
21	chr9:98078212..98082706-chr9:98271985..98275473,10	K562	blood:
22	chr9:98272365..98275151-chr9:98293260..98296891,4	K562	blood:
23	chr9:98271686..98274631-chr9:98635342..98639467,4	MCF-7	breast:
24	chr9:97950616..97952464-chr9:98272435..98274822,2	K562	blood:
25	chr9:98184189..98187188-chr9:98271024..98273730,2	K562	blood:
26	chr9:98265986..98270733-chr9:98272060..98274665,7	MCF-7	breast:
27	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271659	TF binding region
PTCH1	TF binding region
ENSG00000185920	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10512248	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355619	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355620	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909919	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066829	0.83[ASN][1000 genomes]
rs2236407	0.83[ASN][1000 genomes]
rs2282042	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2297086	0.83[ASN][1000 genomes]
rs2297088	0.83[ASN][1000 genomes]
rs28457763	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495472	0.83[ASN][1000 genomes]
rs28496034	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28504650	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28536201	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557305	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28591501	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28620668	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629854	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448343	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119276	0.92[AFR][1000 genomes];0.81[AMR][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	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	esv3421348	chr9:98272156-98274704	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv3424610	chr9:98272481-98274629	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98266600-98275000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr9:98267000-98274800	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr9:98267200-98273600	Active TSS	Right Atrium	heart
4	chr9:98267200-98274000	Active TSS	Fetal Intestine Large	intestine
5	chr9:98267200-98274200	Active TSS	Left Ventricle	heart
6	chr9:98267200-98274400	Active TSS	Ovary	ovary
7	chr9:98267400-98273800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:98267400-98273800	Active TSS	Fetal Intestine Small	intestine
9	chr9:98267400-98273800	Active TSS	Fetal Kidney	kidney
10	chr9:98267400-98273800	Active TSS	Small Intestine	intestine
11	chr9:98267400-98274000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:98267400-98274400	Active TSS	NHDF-Ad	bronchial
13	chr9:98267400-98274600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:98267400-98274800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:98267600-98274000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr9:98267600-98274000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr9:98267600-98274000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:98267600-98274000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:98267600-98274000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:98267600-98274000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:98267600-98274000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:98267600-98274000	Active TSS	Psoas Muscle	Psoas
23	chr9:98267600-98274200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:98267600-98274400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:98267600-98274400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:98267600-98274600	Active TSS	NHLF	lung
27	chr9:98267600-98274800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:98267800-98273600	Active TSS	Lung	lung
29	chr9:98267800-98273800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:98267800-98273800	Active TSS	Duodenum Mucosa	Duodenum
31	chr9:98267800-98273800	Active TSS	HSMMtube	muscle
32	chr9:98267800-98274000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:98267800-98274000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:98267800-98274000	Active TSS	Placenta Amnion	Placenta Amnion
35	chr9:98267800-98274000	Active TSS	A549	lung
36	chr9:98267800-98274200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr9:98267800-98274200	Active TSS	Aorta	Aorta
38	chr9:98267800-98274200	Active TSS	Brain Cingulate Gyrus	brain
39	chr9:98267800-98274200	Active TSS	Brain Hippocampus Middle	brain
40	chr9:98267800-98274200	Active TSS	Brain Substantia Nigra	brain
41	chr9:98267800-98274200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr9:98267800-98274200	Active TSS	Right Ventricle	heart
43	chr9:98267800-98274400	Active TSS	Pancreas	Pancrea
44	chr9:98267800-98274600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr9:98267800-98274600	Active TSS	Brain Angular Gyrus	brain
46	chr9:98267800-98274600	Active TSS	Brain Anterior Caudate	brain
47	chr9:98267800-98274600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr9:98267800-98274800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:98267800-98275000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:98268000-98273600	Active TSS	Cortex derived primary cultured neurospheres	brain

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