Variant report

Variant	rs12123601
Chromosome Location	chr1:113614497-113614498
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	JUN	chr1:113614096-113617273	K562	blood:	n/a	chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097
2	CUX1	chr1:113614496-113616224	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113614064..113616964-chr1:113668302..113669880,2	K562	blood:
2	chr1:113613175..113615596-chr1:113621813..113624852,3	K562	blood:
3	chr1:113493791..113500715-chr1:113613796..113618010,15	K562	blood:
4	chr1:113495059..113500488-chr1:113613593..113618010,11	K562	blood:
5	chr1:113610863..113612583-chr1:113613310..113615320,3	K562	blood:

Variant related genes	Relation type
LRIG2	TF binding region
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000237278	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
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]
rs12117273	1.00[EUR][1000 genomes]
rs12118061	0.83[EUR][1000 genomes]
rs12118532	1.00[AMR][1000 genomes];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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12123519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12125675	0.83[EUR][1000 genomes]
rs12125708	0.83[EUR][1000 genomes]
rs12126304	0.83[EUR][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[EUR][1000 genomes]
rs12136395	0.83[EUR][1000 genomes]
rs12136941	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes]
rs12137299	1.00[EUR][1000 genomes]
rs12139726	0.83[EUR][1000 genomes]
rs12139899	0.83[EUR][1000 genomes]
rs12140067	0.86[EUR][1000 genomes]
rs12140810	0.83[EUR][1000 genomes]
rs12141415	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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]
rs12143341	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12143430	0.83[EUR][1000 genomes]
rs12145713	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12145738	0.83[EUR][1000 genomes]
rs1216767	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1216769	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1216793	1.00[TSI][hapmap];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[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1216812	0.86[EUR][1000 genomes]
rs1216813	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes]
rs12184272	1.00[EUR][1000 genomes]
rs12184320	1.00[EUR][1000 genomes]
rs12744661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1728240	0.86[EUR][1000 genomes]
rs1766864	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][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]
rs4839291	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4839292	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6670587	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6695183	1.00[CEU][hapmap];1.00[EUR][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]
rs7538813	0.86[EUR][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]
rs9429503	1.00[TSI][hapmap]
rs946215	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv508537	chr1:113590343-113635803	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	esv2474740	chr1:113609678-113614799	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv435694	chr1:113610263-113616294	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	esv3523036	chr1:113610983-113615192	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	esv2497412	chr1:113611029-113614851	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113600400-113614800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:113600400-113615000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:113602400-113615000	Weak transcription	Right Atrium	heart
4	chr1:113602600-113614800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:113611200-113614800	Weak transcription	A549	lung
6	chr1:113614200-113614600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:113614200-113614800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:113614200-113614800	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:113614200-113614800	Enhancers	Fetal Heart	heart
10	chr1:113614200-113614800	Enhancers	K562	blood
11	chr1:113614200-113615000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:113614200-113615000	Enhancers	Fetal Intestine Small	intestine
13	chr1:113614400-113614600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:113614400-113614600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:113614400-113614600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:113614400-113614600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:113614400-113614600	Enhancers	HepG2	liver
18	chr1:113614400-113614800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:113614400-113614800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:113614400-113614800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:113614400-113614800	Enhancers	Liver	Liver
22	chr1:113614400-113614800	Enhancers	Dnd41	blood
23	chr1:113614400-113615000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:113614400-113615000	Enhancers	Fetal Intestine Large	intestine
25	chr1:113614400-113615000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:113614400-113615200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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