Variant report

Variant	rs1728240
Chromosome Location	chr1:113617268-113617269
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	RUNX3	chr1:113616713-113617274	GM12878	blood:	n/a	n/a
2	JUN	chr1:113614096-113617273	K562	blood:	n/a	chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097 chr1:113617087-113617097
3	RUNX3	chr1:113616837-113617309	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113442578..113444928-chr1:113615994..113617542,2	K562	blood:
2	chr1:113616013..113618025-chr1:113688637..113691001,2	MCF-7	breast:
3	chr1:113493791..113500715-chr1:113613796..113618010,15	K562	blood:
4	chr1:113615667..113617631-chr6:26055280..26057308,2	MCF-7	breast:
5	chr1:113615839..113617741-chr1:113618615..113621229,2	K562	blood:
6	chr1:113615878..113618493-chr1:113649795..113652119,3	MCF-7	breast:
7	chr1:113495059..113500488-chr1:113613593..113618010,11	K562	blood:
8	chr1:113258208..113260404-chr1:113615515..113617358,3	MCF-7	breast:
9	chr1:113615969..113617756-chr1:113641102..113642672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238198	TF binding region
ENSG00000187837	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000226419	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11102586	0.86[EUR][1000 genomes]
rs12071491	1.00[EUR][1000 genomes]
rs12117273	0.86[EUR][1000 genomes]
rs12118532	0.86[EUR][1000 genomes]
rs12120738	0.86[EUR][1000 genomes]
rs12123072	0.86[EUR][1000 genomes]
rs12123519	0.86[EUR][1000 genomes]
rs12123601	0.86[EUR][1000 genomes]
rs12128658	0.86[EUR][1000 genomes]
rs12133057	0.86[EUR][1000 genomes]
rs12136941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12137299	0.86[EUR][1000 genomes]
rs12140067	1.00[EUR][1000 genomes]
rs12141415	0.86[EUR][1000 genomes]
rs12143171	0.86[EUR][1000 genomes]
rs12143341	0.86[EUR][1000 genomes]
rs1216767	0.86[EUR][1000 genomes]
rs1216769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1216802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1216807	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1216808	0.86[EUR][1000 genomes]
rs1216810	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1216812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1216813	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12184272	0.86[EUR][1000 genomes]
rs12184320	0.86[EUR][1000 genomes]
rs12744661	0.86[EUR][1000 genomes]
rs1310142	0.86[EUR][1000 genomes]
rs1618794	0.86[EUR][1000 genomes]
rs17031006	0.86[EUR][1000 genomes]
rs1728229	0.86[EUR][1000 genomes]
rs1766864	0.86[EUR][1000 genomes]
rs1778017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1778019	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670587	1.00[EUR][1000 genomes]
rs6695183	0.86[EUR][1000 genomes]
rs7545814	1.00[EUR][1000 genomes]
rs946215	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113615000-113617400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:113615000-113617400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:113615000-113617400	Active TSS	Colonic Mucosa	Colon
4	chr1:113615000-113617400	Active TSS	NHLF	lung
5	chr1:113615000-113617800	Active TSS	Right Ventricle	heart
6	chr1:113615200-113617400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:113615200-113617400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:113615200-113617400	Active TSS	HSMM	muscle
9	chr1:113615200-113617600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:113615200-113617800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:113615200-113618000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:113615200-113618200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:113615400-113618000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:113616400-113617400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:113616400-113617800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:113616600-113617400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:113616600-113617400	Flanking Active TSS	Hela-S3	cervix
18	chr1:113616800-113617400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:113616800-113617400	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:113616800-113617400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:113616800-113617400	Flanking Active TSS	HMEC	breast
22	chr1:113616800-113617400	Flanking Active TSS	NHEK	skin
23	chr1:113616800-113617600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:113616800-113617800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:113616800-113617800	Enhancers	Gastric	stomach
26	chr1:113616800-113617800	Enhancers	Pancreas	Pancrea
27	chr1:113616800-113617800	Enhancers	Spleen	Spleen
28	chr1:113616800-113618200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:113616800-113619400	Weak transcription	Placenta	Placenta
30	chr1:113616800-113621400	Weak transcription	Lung	lung
31	chr1:113616800-113625600	Weak transcription	Esophagus	oesophagus
32	chr1:113616800-113638600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:113617000-113617400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:113617000-113617400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:113617000-113617600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:113617000-113617800	Enhancers	Primary B cells from cord blood	blood
37	chr1:113617000-113617800	Enhancers	Fetal Muscle Leg	muscle
38	chr1:113617000-113617800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:113617000-113618000	Weak transcription	Brain Substantia Nigra	brain
40	chr1:113617000-113618400	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:113617000-113618400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:113617000-113618800	Enhancers	Fetal Thymus	thymus
43	chr1:113617000-113620200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:113617000-113620800	Weak transcription	Fetal Lung	lung
45	chr1:113617000-113630800	Weak transcription	Ovary	ovary
46	chr1:113617000-113636800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:113617000-113636800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:113617000-113638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:113617000-113645800	Weak transcription	Aorta	Aorta
50	chr1:113617200-113617400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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