Variant report

Variant	rs12497444
Chromosome Location	chr3:194931208-194931209
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	NFIC	chr3:194930765-194931517	ECC-1	luminal epithelium:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
2	MEF2A	chr3:194931131-194931518	K562	blood:	n/a	chr3:194931386-194931407 chr3:194931388-194931403 chr3:194931388-194931402 chr3:194931390-194931401 chr3:194931386-194931407 chr3:194931386-194931407 chr3:194931387-194931404 chr3:194931391-194931400 chr3:194931387-194931403
3	TCF12	chr3:194930437-194931947	SK-N-SH	brain:	n/a	chr3:194931446-194931453 chr3:194931206-194931213
4	ESR1	chr3:194930830-194931617	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr3:194930638-194931799	SK-N-SH	brain:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
6	ESR1	chr3:194930853-194931597	ECC-1	luminal epithelium:	n/a	n/a
7	ESR1	chr3:194930797-194931563	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr3:194930532-194931905	SK-N-SH	brain:	n/a	chr3:194931446-194931453 chr3:194931206-194931213
9	NFIC	chr3:194930487-194931928	SK-N-SH	brain:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
10	MEF2A	chr3:194931023-194931771	SK-N-SH	brain:	n/a	chr3:194931386-194931407 chr3:194931388-194931403 chr3:194931388-194931402 chr3:194931390-194931401 chr3:194931386-194931407 chr3:194931386-194931407 chr3:194931387-194931404 chr3:194931391-194931400 chr3:194931387-194931403
11	MEF2A	chr3:194930955-194931870	SK-N-SH	brain:	n/a	chr3:194931386-194931407 chr3:194931388-194931403 chr3:194931388-194931402 chr3:194931390-194931401 chr3:194931386-194931407 chr3:194931386-194931407 chr3:194931387-194931404 chr3:194931391-194931400 chr3:194931387-194931403
12	POLR2A	chr3:194931101-194931236	HUVEC	blood vessel:	n/a	n/a
13	NFIC	chr3:194930782-194931656	ECC-1	luminal epithelium:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
14	EP300	chr3:194930487-194931782	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr3:194930723-194931880	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr3:194930965-194931832	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:194931000-194931801	SK-N-SH	brain:	n/a	n/a
18	EP300	chr3:194931007-194931341	SK-N-SH_RA	brain:	n/a	n/a
19	ESR1	chr3:194930831-194931672	ECC-1	luminal epithelium:	n/a	n/a
20	GATA3	chr3:194930868-194931943	SK-N-SH	brain:	n/a	chr3:194931823-194931834

Variant related genes	Relation type
XXYLT1	TF binding region
RNU6-25P	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10933702	0.85[EUR][1000 genomes]
rs10933703	0.85[EUR][1000 genomes]
rs11917438	0.85[EUR][1000 genomes]
rs11918143	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928199	0.90[EUR][1000 genomes]
rs12485800	0.90[EUR][1000 genomes]
rs12486168	0.85[EUR][1000 genomes]
rs12486220	0.85[EUR][1000 genomes]
rs12486636	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486835	0.85[EUR][1000 genomes]
rs12488616	0.95[EUR][1000 genomes]
rs12491426	0.95[EUR][1000 genomes]
rs12491902	0.95[EUR][1000 genomes]
rs12493888	0.95[EUR][1000 genomes]
rs12495659	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12496628	0.90[EUR][1000 genomes]
rs12497906	0.90[EUR][1000 genomes]
rs35899174	0.81[EUR][1000 genomes]
rs3796161	0.91[ASN][1000 genomes]
rs56281422	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56835677	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58113840	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59579668	0.85[EUR][1000 genomes]
rs60677730	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61022222	0.95[EUR][1000 genomes]
rs6437466	0.85[EUR][1000 genomes]
rs66510151	0.95[EUR][1000 genomes]
rs67388686	0.85[EUR][1000 genomes]
rs67413252	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67484513	0.95[EUR][1000 genomes]
rs6777904	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785108	0.81[EUR][1000 genomes]
rs6790425	1.00[EUR][1000 genomes]
rs72499624	0.95[EUR][1000 genomes]
rs72499625	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7642127	0.90[EUR][1000 genomes]
rs999331	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
20	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking 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	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194918800-194945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:194919400-194945200	Weak transcription	Thymus	Thymus
3	chr3:194921000-194941600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:194924600-194931800	Enhancers	Placenta	Placenta
5	chr3:194926400-194931400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:194926400-194942600	Weak transcription	Small Intestine	intestine
7	chr3:194926400-194947600	Weak transcription	Gastric	stomach
8	chr3:194926600-194933400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:194926600-194942800	Weak transcription	Hela-S3	cervix
10	chr3:194927600-194931800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:194927800-194931800	Enhancers	Fetal Thymus	thymus
12	chr3:194928400-194931800	Enhancers	Left Ventricle	heart
13	chr3:194928400-194932000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:194928400-194932000	Enhancers	Brain Germinal Matrix	brain
15	chr3:194928400-194932600	Enhancers	Ovary	ovary
16	chr3:194928400-194932600	Enhancers	NHLF	lung
17	chr3:194928600-194931800	Enhancers	Right Ventricle	heart
18	chr3:194928600-194932200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:194928600-194932400	Enhancers	Fetal Heart	heart
20	chr3:194928600-194932600	Enhancers	Fetal Stomach	stomach
21	chr3:194928600-194933600	Enhancers	Lung	lung
22	chr3:194928800-194931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:194928800-194931800	Enhancers	Brain Hippocampus Middle	brain
24	chr3:194929000-194931400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:194929000-194931400	Enhancers	Brain Anterior Caudate	brain
26	chr3:194929000-194931400	Enhancers	Esophagus	oesophagus
27	chr3:194929000-194931800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:194929000-194931800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:194929000-194931800	Enhancers	K562	blood
30	chr3:194929000-194932400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:194929200-194932400	Enhancers	HUVEC	blood vessel
32	chr3:194929400-194931400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:194929400-194931800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:194929400-194932000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:194929400-194932400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:194929400-194932600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:194929600-194931600	Flanking Active TSS	HSMMtube	muscle
38	chr3:194929600-194931800	Enhancers	Right Atrium	heart
39	chr3:194929600-194932400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:194929800-194931400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr3:194929800-194931600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr3:194929800-194931600	Enhancers	Brain Cingulate Gyrus	brain
43	chr3:194929800-194931600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:194929800-194931600	Enhancers	GM12878-XiMat	blood
45	chr3:194929800-194947400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:194930000-194931400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:194930000-194931600	Enhancers	Brain Substantia Nigra	brain
48	chr3:194930000-194931600	Enhancers	HMEC	breast
49	chr3:194930200-194931400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:194930400-194931400	Enhancers	Brain Angular Gyrus	brain

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