Variant report

Variant	rs12120738
Chromosome Location	chr1:113624181-113624182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113614694..113617981-chr1:113622336..113625985,3	MCF-7	breast:
2	chr1:113614553..113617626-chr1:113623391..113625397,4	MCF-7	breast:
3	chr1:113623954..113625982-chr1:113629801..113631439,2	K562	blood:
4	chr1:113613175..113615596-chr1:113621813..113624852,3	K562	blood:
5	chr1:113622553..113624863-chr1:113644345..113646083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198799	Chromatin interaction
ENSG00000238198	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11102584	1.00[AFR][1000 genomes];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]
rs12117273	1.00[AMR][1000 genomes];1.00[EUR][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]
rs12123072	1.00[EUR][1000 genomes]
rs12123519	1.00[EUR][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]
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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136395	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12136941	0.86[EUR][1000 genomes]
rs12137299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12138968	1.00[AMR][1000 genomes]
rs12139726	0.83[EUR][1000 genomes]
rs12139899	0.83[EUR][1000 genomes]
rs12140067	0.86[EUR][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]
rs12141415	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143341	1.00[EUR][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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12184320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12744661	1.00[EUR][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]
rs4839291	0.86[EUR][1000 genomes]
rs4839292	0.86[EUR][1000 genomes]
rs6670587	0.86[EUR][1000 genomes]
rs6695183	1.00[EUR][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]
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	0.86[EUR][1000 genomes]
rs946215	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	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113616800-113625600	Weak transcription	Esophagus	oesophagus
2	chr1:113616800-113638600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:113617000-113630800	Weak transcription	Ovary	ovary
4	chr1:113617000-113636800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:113617000-113636800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:113617000-113638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113617000-113645800	Weak transcription	Aorta	Aorta
8	chr1:113617200-113630400	Weak transcription	Fetal Kidney	kidney
9	chr1:113617200-113631200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:113617200-113631600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:113617200-113633800	Weak transcription	Liver	Liver
12	chr1:113617200-113635800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:113617200-113636400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:113617200-113636400	Weak transcription	HSMMtube	muscle
15	chr1:113617200-113636400	Weak transcription	NHDF-Ad	bronchial
16	chr1:113617200-113642600	Weak transcription	A549	lung
17	chr1:113617400-113624600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:113617400-113624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:113617400-113634600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:113617400-113638000	Weak transcription	NHLF	lung
21	chr1:113617800-113628000	Weak transcription	Primary B cells from cord blood	blood
22	chr1:113617800-113634600	Weak transcription	NHEK	skin
23	chr1:113617800-113637200	Weak transcription	Psoas Muscle	Psoas
24	chr1:113617800-113637800	Weak transcription	Spleen	Spleen
25	chr1:113617800-113638000	Weak transcription	Gastric	stomach
26	chr1:113618000-113634200	Weak transcription	Hela-S3	cervix
27	chr1:113618200-113629000	Weak transcription	Fetal Heart	heart
28	chr1:113618200-113631600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:113618200-113631600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:113618400-113624600	Weak transcription	Primary T cells from cord blood	blood
31	chr1:113618400-113627400	Weak transcription	HUVEC	blood vessel
32	chr1:113618400-113631600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:113618400-113634200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:113618400-113634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:113618800-113629600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:113619000-113631200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:113619000-113633600	Weak transcription	HepG2	liver
38	chr1:113619200-113625800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:113619400-113624800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:113619400-113626400	Strong transcription	Fetal Stomach	stomach
41	chr1:113619400-113630200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:113619400-113631400	Weak transcription	Brain Angular Gyrus	brain
43	chr1:113619600-113628200	Strong transcription	Fetal Intestine Small	intestine
44	chr1:113619600-113630800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:113619600-113631600	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:113619600-113636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:113619800-113625400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:113619800-113626000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:113619800-113626400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:113619800-113626400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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