Variant report

Variant	rs12631534
Chromosome Location	chr3:194872731-194872732
allele	A/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	chr3:194872407-194873572	HUVEC	blood vessel:	n/a	n/a
2	USF2	chr3:194872731-194872897	HepG2	liver:	n/a	chr3:194872787-194872798
3	USF1	chr3:194872632-194872893	A549	lung:	n/a	n/a
4	USF2	chr3:194872722-194872887	Hela-S3	cervix:	n/a	chr3:194872787-194872798
5	ATF1	chr3:194872688-194872871	K562	blood:	n/a	n/a
6	POLR2A	chr3:194872570-194873617	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:194872361-194874182	HUVEC	blood vessel:	n/a	n/a
8	FOSL1	chr3:194872579-194873147	HCT-116	colon:	n/a	n/a
9	STAT3	chr3:194872617-194872881	MCF10A-Er-Src	breast:	n/a	n/a
10	ARID3A	chr3:194872565-194872765	K562	blood:	n/a	n/a
11	JUN	chr3:194872400-194873325	K562	blood:	n/a	n/a
12	USF1	chr3:194872646-194872861	H1-hESC	embryonic stem cell:	n/a	n/a
13	STAT3	chr3:194872555-194872933	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:194872614-194873243	HUVEC	blood vessel:	n/a	n/a
15	STAT3	chr3:194872546-194872934	MCF10A-Er-Src	breast:	n/a	n/a
16	JUN	chr3:194872634-194873076	K562	blood:	n/a	n/a
17	MAZ	chr3:194872655-194872803	K562	blood:	n/a	n/a
18	USF1	chr3:194872666-194872901	SK-N-SH_RA	brain:	n/a	n/a
19	FOS	chr3:194872592-194873002	MCF10A-Er-Src	breast:	n/a	chr3:194872773-194872784
20	FOS	chr3:194872606-194872987	MCF10A-Er-Src	breast:	n/a	chr3:194872773-194872784
21	USF1	chr3:194872631-194873090	HCT-116	colon:	n/a	n/a
22	MYC	chr3:194872654-194872935	MCF10A-Er-Src	breast:	n/a	n/a
23	EP300	chr3:194872727-194872891	K562	blood:	n/a	n/a
24	FOS	chr3:194872625-194872978	MCF10A-Er-Src	breast:	n/a	chr3:194872773-194872784
25	TBL1XR1	chr3:194872681-194872856	K562	blood:	n/a	n/a
26	MAX	chr3:194872650-194872975	K562	blood:	n/a	n/a
27	USF1	chr3:194872648-194872873	SK-N-SH_RA	brain:	n/a	n/a
28	POLR2A	chr3:194872405-194873627	HUVEC	blood vessel:	n/a	n/a
29	USF1	chr3:194872640-194872991	K562	blood:	n/a	n/a
30	USF1	chr3:194872697-194872973	SK-N-SH	brain:	n/a	n/a
31	USF2	chr3:194872624-194872824	GM12878	blood:	n/a	chr3:194872787-194872798
32	FOS	chr3:194872634-194872964	MCF10A-Er-Src	breast:	n/a	chr3:194872773-194872784
33	MAX	chr3:194872620-194872996	HUVEC	blood vessel:	n/a	n/a
34	GATA2	chr3:194872627-194873180	HUVEC	blood vessel:	n/a	n/a
35	JUN	chr3:194872581-194873207	HUVEC	blood vessel:	n/a	n/a
36	FOS	chr3:194872580-194873195	HUVEC	blood vessel:	n/a	chr3:194872773-194872784
37	CEBPB	chr3:194872576-194872919	IMR90	lung:	n/a	n/a
38	JUND	chr3:194872656-194872936	K562	blood:	n/a	n/a
39	MYC	chr3:194872712-194872941	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194871135..194873773-chr3:194909112..194911185,2	K562	blood:
2	chr3:194838435..194840732-chr3:194871464..194873939,2	K562	blood:
3	chr3:194870603..194872968-chr3:194930308..194933039,3	K562	blood:
4	chr3:194867331..194869999-chr3:194871717..194874050,2	MCF-7	breast:
5	chr3:194870056..194873329-chr3:194873550..194878227,7	K562	blood:

Variant related genes	Relation type
RN7SL36P	TF binding region
ENSG00000230266	Chromatin interaction
ENSG00000173950	Chromatin interaction
ENSG00000244314	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12490970	0.96[ASN][1000 genomes]
rs12634183	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794662	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628353	0.92[ASN][1000 genomes]
rs9830280	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9841564	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
3	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:194862400-194897800	Weak transcription	Dnd41	blood
6	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
7	chr3:194868400-194877400	Enhancers	Fetal Heart	heart
8	chr3:194868800-194875000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
10	chr3:194869600-194876400	Enhancers	NHDF-Ad	bronchial
11	chr3:194869800-194876600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:194870800-194877600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:194871000-194873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:194871000-194877200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:194871000-194880800	Enhancers	HUVEC	blood vessel
16	chr3:194871200-194873600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:194871400-194875800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:194871400-194877800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:194871600-194873000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:194871600-194873400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:194871600-194873600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:194871600-194874600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:194871600-194875000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:194871600-194875200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:194871600-194875800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:194871600-194876000	Enhancers	NHEK	skin
28	chr3:194871600-194877600	Enhancers	Fetal Intestine Large	intestine
29	chr3:194871600-194881200	Weak transcription	Liver	Liver
30	chr3:194871800-194872800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:194871800-194872800	Weak transcription	Fetal Lung	lung
32	chr3:194871800-194873000	Weak transcription	Ovary	ovary
33	chr3:194871800-194873000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:194871800-194873000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:194871800-194873200	Weak transcription	Brain Anterior Caudate	brain
36	chr3:194871800-194873600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:194871800-194873600	Weak transcription	Fetal Brain Female	brain
38	chr3:194871800-194873800	Weak transcription	Brain Angular Gyrus	brain
39	chr3:194871800-194873800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:194871800-194873800	Weak transcription	Brain Substantia Nigra	brain
41	chr3:194871800-194873800	Weak transcription	Gastric	stomach
42	chr3:194871800-194873800	Enhancers	Stomach Smooth Muscle	stomach
43	chr3:194871800-194873800	Weak transcription	Spleen	Spleen
44	chr3:194871800-194874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:194871800-194874800	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:194871800-194875000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:194871800-194875000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:194871800-194875200	Enhancers	K562	blood
49	chr3:194871800-194875400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:194871800-194875600	Enhancers	NHLF	lung

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