Variant report

Variant	rs12143341
Chromosome Location	chr1:113573797-113573798
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	NFATC1	chr1:113573714-113574425	GM12878	blood:	n/a	n/a
2	STAT5A	chr1:113573776-113574250	GM12878	blood:	n/a	chr1:113573850-113573858
3	PML	chr1:113573727-113574368	GM12878	blood:	n/a	n/a
4	SPI1	chr1:113573777-113574184	GM12891	blood:	n/a	n/a
5	CEBPB	chr1:113573763-113574379	GM12878	blood:	n/a	n/a
6	BATF	chr1:113573777-113574227	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:113573783-113574014	HUVEC	blood vessel:	n/a	n/a
8	IKZF1	chr1:113573689-113574230	GM12878	blood:	n/a	n/a
9	TCF3	chr1:113573777-113574258	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:113573731-113574028	Hela-S3	cervix:	n/a	n/a
11	FOXM1	chr1:113573777-113574393	GM12878	blood:	n/a	n/a
12	NFIC	chr1:113573663-113574451	GM12878	blood:	n/a	n/a
13	JUND	chr1:113573535-113574432	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:113573722-113574334	GM12892	blood:	n/a	n/a
15	RUNX3	chr1:113573788-113574268	GM12878	blood:	n/a	n/a
16	RUNX3	chr1:113573715-113574376	GM12878	blood:	n/a	n/a
17	IRF4	chr1:113573752-113574389	GM12878	blood:	n/a	n/a
18	MTA3	chr1:113573694-113574298	GM12878	blood:	n/a	n/a
19	ATF2	chr1:113573751-113574402	GM12878	blood:	n/a	n/a
20	FOXM1	chr1:113573698-113574385	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113570114..113572755-chr1:113573147..113575592,2	K562	blood:
2	chr1:113572393..113574061-chr1:113600793..113602856,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236066	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11102561	1.00[ASN][1000 genomes]
rs11102586	1.00[EUR][1000 genomes]
rs11102588	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11102592	1.00[CEU][hapmap]
rs12071491	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117273	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118061	0.83[EUR][1000 genomes]
rs12118532	1.00[EUR][1000 genomes]
rs12119387	0.83[EUR][1000 genomes]
rs12120401	0.83[EUR][1000 genomes]
rs12120441	0.83[EUR][1000 genomes]
rs12120738	1.00[EUR][1000 genomes]
rs12123072	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123519	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123601	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12125675	0.83[EUR][1000 genomes]
rs12125708	0.83[EUR][1000 genomes]
rs12126304	0.83[EUR][1000 genomes]
rs12126316	1.00[ASN][1000 genomes]
rs12127415	0.83[EUR][1000 genomes]
rs12128658	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12129858	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12133057	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136395	0.83[EUR][1000 genomes]
rs12136941	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12137299	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138968	1.00[ASN][1000 genomes]
rs12139726	0.83[EUR][1000 genomes]
rs12139899	0.83[EUR][1000 genomes]
rs12140067	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140810	0.83[EUR][1000 genomes]
rs12141018	1.00[ASN][1000 genomes]
rs12141415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141540	0.83[EUR][1000 genomes]
rs12141541	0.83[EUR][1000 genomes]
rs12142449	0.83[EUR][1000 genomes]
rs12142475	0.83[EUR][1000 genomes]
rs12142510	0.83[EUR][1000 genomes]
rs12143171	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143430	0.83[EUR][1000 genomes]
rs12145713	0.83[EUR][1000 genomes]
rs12145738	0.83[EUR][1000 genomes]
rs1216767	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1216769	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1216793	0.86[EUR][1000 genomes]
rs1216798	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1216802	0.86[EUR][1000 genomes]
rs1216807	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1216808	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1216812	0.86[EUR][1000 genomes]
rs1216813	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12184272	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184320	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744661	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1310142	1.00[EUR][1000 genomes]
rs1618794	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17031006	1.00[EUR][1000 genomes]
rs1728227	0.86[EUR][1000 genomes]
rs1728229	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1728240	0.86[EUR][1000 genomes]
rs1766864	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1766865	1.00[CEU][hapmap]
rs1778016	0.86[EUR][1000 genomes]
rs1778017	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1778019	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs41296184	0.86[EUR][1000 genomes]
rs41306207	1.00[ASN][1000 genomes]
rs4839291	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4839292	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56335344	1.00[ASN][1000 genomes]
rs6665673	1.00[ASN][1000 genomes]
rs6670587	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6695183	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72982435	1.00[ASN][1000 genomes]
rs72982438	1.00[ASN][1000 genomes]
rs73000320	1.00[ASN][1000 genomes]
rs73000335	1.00[ASN][1000 genomes]
rs74111210	0.86[EUR][1000 genomes]
rs74111213	0.86[EUR][1000 genomes]
rs7518115	0.83[EUR][1000 genomes]
rs7531847	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7535389	1.00[ASN][1000 genomes]
rs7538813	0.86[EUR][1000 genomes]
rs7541119	1.00[ASN][1000 genomes]
rs7541246	0.83[EUR][1000 genomes]
rs7541520	0.83[EUR][1000 genomes]
rs7541703	0.83[EUR][1000 genomes]
rs7545814	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429503	1.00[ASN][1000 genomes]
rs946215	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	esv990846	chr1:113573220-113576139	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
2	chr1:113543200-113574400	Weak transcription	HSMM	muscle
3	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:113562400-113574000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:113564600-113577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:113564600-113577600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:113564800-113579400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:113564800-113583000	Weak transcription	Stomach Mucosa	stomach
9	chr1:113570200-113575000	Enhancers	Liver	Liver
10	chr1:113570400-113579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:113570600-113575200	Enhancers	HepG2	liver
12	chr1:113571000-113574400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:113571200-113579600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:113571400-113579200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:113571600-113579400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:113571600-113584000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:113572000-113579400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:113572400-113574200	Enhancers	Fetal Heart	heart
19	chr1:113572600-113574800	Enhancers	GM12878-XiMat	blood
20	chr1:113572600-113579200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:113572600-113579200	Weak transcription	Thymus	Thymus
22	chr1:113572600-113584600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:113573200-113573800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:113573200-113574400	Enhancers	HUVEC	blood vessel
25	chr1:113573400-113573800	Weak transcription	Fetal Intestine Small	intestine
26	chr1:113573600-113573800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr1:113573600-113573800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:113573600-113574000	Enhancers	Left Ventricle	heart

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