Variant report

Variant	rs12137299
Chromosome Location	chr1:113580385-113580386
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113422315..113424969-chr1:113580165..113583110,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-5	chr1:113577443-113580582	NONHSAT005312

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11102561	1.00[ASN][1000 genomes]
rs11102584	1.00[AMR][1000 genomes]
rs11102586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11102588	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12071491	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118061	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12118532	1.00[EUR][1000 genomes]
rs12118642	1.00[AMR][1000 genomes]
rs12119387	0.83[EUR][1000 genomes]
rs12120401	0.83[EUR][1000 genomes]
rs12120441	0.83[EUR][1000 genomes]
rs12120738	1.00[AMR][1000 genomes];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[EUR][1000 genomes]
rs12125675	0.83[EUR][1000 genomes]
rs12125708	0.83[EUR][1000 genomes]
rs12126304	0.83[EUR][1000 genomes]
rs12126316	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12127415	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12128658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129858	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12133057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136395	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12136941	0.86[EUR][1000 genomes]
rs12138968	1.00[AMR][1000 genomes];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]
rs12140651	1.00[AMR][1000 genomes]
rs12140676	1.00[AMR][1000 genomes]
rs12140810	0.83[EUR][1000 genomes]
rs12141018	1.00[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143341	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143430	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145713	0.83[EUR][1000 genomes]
rs12145738	0.83[EUR][1000 genomes]
rs1216767	1.00[EUR][1000 genomes]
rs1216769	0.86[EUR][1000 genomes]
rs1216793	0.86[EUR][1000 genomes]
rs1216798	0.86[EUR][1000 genomes]
rs1216802	0.86[EUR][1000 genomes]
rs1216807	0.86[EUR][1000 genomes]
rs1216808	1.00[EUR][1000 genomes]
rs1216812	0.86[EUR][1000 genomes]
rs1216813	0.86[EUR][1000 genomes]
rs12184272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184320	1.00[AFR][1000 genomes];1.00[AMR][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[EUR][1000 genomes]
rs17031006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1728227	0.86[EUR][1000 genomes]
rs1728229	1.00[EUR][1000 genomes]
rs1728240	0.86[EUR][1000 genomes]
rs1766864	1.00[EUR][1000 genomes]
rs1778016	0.86[EUR][1000 genomes]
rs1778017	0.86[EUR][1000 genomes]
rs1778019	0.86[EUR][1000 genomes]
rs41296184	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41306207	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4839291	0.86[EUR][1000 genomes]
rs4839292	0.86[EUR][1000 genomes]
rs56335344	1.00[ASN][1000 genomes]
rs6665673	1.00[ASN][1000 genomes]
rs6670587	0.86[EUR][1000 genomes]
rs6695183	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	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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429503	1.00[ASN][1000 genomes]
rs946215	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:113564800-113583000	Weak transcription	Stomach Mucosa	stomach
3	chr1:113571600-113584000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:113572600-113584600	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:113573800-113584200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:113574000-113582200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:113578000-113584800	Weak transcription	Hela-S3	cervix
8	chr1:113579400-113580600	Enhancers	HepG2	liver
9	chr1:113579600-113584000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:113579600-113584200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:113579800-113583400	Weak transcription	NHEK	skin
12	chr1:113579800-113583600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:113579800-113584400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:113579800-113584400	Weak transcription	Osteobl	bone
15	chr1:113579800-113584600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:113579800-113584600	Weak transcription	NHDF-Ad	bronchial
17	chr1:113579800-113584800	Weak transcription	Psoas Muscle	Psoas
18	chr1:113580000-113583000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:113580000-113583200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:113580000-113583600	Weak transcription	GM12878-XiMat	blood
21	chr1:113580000-113583800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:113580000-113584000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:113580000-113584400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:113580000-113584400	Weak transcription	Fetal Thymus	thymus
25	chr1:113580200-113582000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:113580200-113582200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:113580200-113582600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:113580200-113582800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:113580200-113583000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:113580200-113583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:113580200-113584200	Weak transcription	HMEC	breast
32	chr1:113580200-113589200	Weak transcription	Right Atrium	heart

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