Variant report

Variant	rs116220656
Chromosome Location	chr1:228674728-228674729
allele	C/G
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	POLR2A	chr1:228674325-228674771	GM12878	blood:	n/a	n/a
2	RFX5	chr1:228673704-228675743	IMR90	lung:	n/a	chr1:228674183-228674198
3	CREB1	chr1:228674063-228675219	GM12878	blood:	n/a	n/a
4	TCF12	chr1:228674643-228674832	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr1:228674273-228675985	K562	blood:	n/a	chr1:228675761-228675771
6	TCF12	chr1:228674615-228675005	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP4	chr1:228674545-228675049	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF2	chr1:228674483-228675022	H1-hESC	embryonic stem cell:	n/a	n/a
9	CBX3	chr1:228674507-228675085	K562	blood:	n/a	n/a
10	POLR2A	chr1:228674383-228675287	SK-N-MC	brain:	n/a	n/a
11	CHD1	chr1:228674193-228674928	GM12878	blood:	n/a	n/a
12	USF2	chr1:228674424-228675065	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr1:228674407-228674970	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:228674254-228675474	MCF-7	breast:	n/a	n/a
15	SMC3	chr1:228674267-228674999	K562	blood:	n/a	n/a
16	SIN3A	chr1:228674089-228675493	H1-hESC	embryonic stem cell:	n/a	chr1:228675461-228675472 chr1:228674871-228674882 chr1:228675386-228675399 chr1:228675388-228675399
17	CREB1	chr1:228674393-228675159	ECC-1	luminal epithelium:	n/a	n/a
18	MYC	chr1:228674699-228675093	MCF-7	breast:	n/a	n/a
19	REST	chr1:228674699-228675201	PFSK-1	brain:	n/a	n/a
20	NFIC	chr1:228674540-228675027	HepG2	liver:	n/a	n/a
21	ZNF143	chr1:228674368-228675180	K562	blood:	n/a	n/a
22	MAX	chr1:228674036-228675210	ECC-1	luminal epithelium:	n/a	n/a
23	ATF2	chr1:228674256-228675042	GM12878	blood:	n/a	n/a
24	PML	chr1:228674368-228674802	GM12878	blood:	n/a	n/a
25	GTF2F1	chr1:228674560-228675019	K562	blood:	n/a	n/a
26	MYC	chr1:228674356-228675475	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr1:228674196-228675004	GM12878	blood:	n/a	n/a
28	BACH1	chr1:228674184-228675065	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr1:228674046-228675272	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr1:228674195-228675369	HUVEC	blood vessel:	n/a	n/a
31	BHLHE40	chr1:228674214-228675144	K562	blood:	n/a	n/a
32	MYC	chr1:228674309-228675125	HUVEC	blood vessel:	n/a	n/a
33	NFATC1	chr1:228674322-228674828	GM12878	blood:	n/a	n/a
34	MAZ	chr1:228674322-228675843	Hela-S3	cervix:	n/a	chr1:228675761-228675771
35	GABPA	chr1:228674669-228675292	H1-hESC	embryonic stem cell:	n/a	chr1:228675176-228675185
36	IRF1	chr1:228674324-228675256	K562	blood:	n/a	chr1:228674668-228674682 chr1:228674671-228674683
37	UBTF	chr1:228674534-228676112	K562	blood:	n/a	n/a
38	MAX	chr1:228674385-228675400	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:228674145-228676899	K562	blood:	n/a	n/a
40	ZNF143	chr1:228674179-228675477	GM12878	blood:	n/a	chr1:228675175-228675185
41	SP1	chr1:228674046-228675375	HCT-116	colon:	n/a	chr1:228674571-228674585
42	FOXM1	chr1:228674142-228675108	GM12878	blood:	n/a	n/a
43	MAFK	chr1:228674232-228675014	K562	blood:	n/a	n/a
44	EGR1	chr1:228674156-228675067	K562	blood:	n/a	chr1:228674549-228674559
45	CREB1	chr1:228674509-228675114	ECC-1	luminal epithelium:	n/a	n/a
46	EGR1	chr1:228674133-228675072	ECC-1	luminal epithelium:	n/a	chr1:228674549-228674559
47	NRF1	chr1:228674621-228674974	K562	blood:	n/a	chr1:228674781-228674792
48	TBL1XR1	chr1:228674254-228675132	K562	blood:	n/a	n/a
49	REST	chr1:228674725-228675410	PFSK-1	brain:	n/a	chr1:228675288-228675301 chr1:228675360-228675373
50	HDAC2	chr1:228674155-228674945	MCF-7	breast:	n/a	chr1:228674615-228674634

No.	Distal block	Cell Line	Cell type
1	chr1:11967567..11969704-chr1:228673208..228675906,2	MCF-7	breast:
2	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
3	chr1:228674158..228676652-chr1:228698714..228701340,3	K562	blood:
4	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
5	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
6	chr1:228645191..228645823-chr1:228674602..228675559,2	K562	blood:
7	chr1:228487271..228488896-chr1:228674554..228676402,2	K562	blood:
8	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
9	chr1:228673229..228674751-chr9:33024497..33026836,2	MCF-7	breast:
10	chr1:228645158..228646173-chr1:228673944..228674999,3	Hela-S3	cervix:
11	chr1:228321585..228323850-chr1:228673376..228675624,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP5-915N17.9.1-2	chr1:228673895-228674821	NONHSAT010027

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000168159	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000086061	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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 miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
12	esv3417507	chr1:228673529-228677127	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	esv3338881	chr1:228674354-228676902	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	esv3408363	chr1:228674504-228676727	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228673600-228675800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:228673600-228675800	Active TSS	K562	blood
3	chr1:228673600-228676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:228673600-228676000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:228673600-228676000	Active TSS	A549	lung
6	chr1:228673600-228676000	Active TSS	Hela-S3	cervix
7	chr1:228673600-228676200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:228673800-228674800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:228673800-228675600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:228673800-228675800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:228673800-228675800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:228673800-228675800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:228673800-228675800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:228673800-228675800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:228673800-228675800	Active TSS	Brain Hippocampus Middle	brain
16	chr1:228673800-228675800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:228673800-228675800	Active TSS	Fetal Muscle Leg	muscle
18	chr1:228673800-228675800	Active TSS	GM12878-XiMat	blood
19	chr1:228673800-228676000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:228673800-228676000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:228673800-228676000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:228673800-228676000	Active TSS	Primary T cells from cord blood	blood
23	chr1:228673800-228676000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:228673800-228676000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:228673800-228676000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:228673800-228676000	Active TSS	Aorta	Aorta
27	chr1:228673800-228676000	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:228673800-228676000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:228673800-228676000	Active TSS	Colon Smooth Muscle	Colon
30	chr1:228673800-228676000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:228673800-228676000	Active TSS	Fetal Intestine Large	intestine
32	chr1:228673800-228676000	Active TSS	Psoas Muscle	Psoas
33	chr1:228673800-228676000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:228673800-228676000	Active TSS	Rectal Smooth Muscle	rectum
35	chr1:228673800-228676000	Active TSS	NHEK	skin
36	chr1:228673800-228676200	Active TSS	Brain Angular Gyrus	brain
37	chr1:228673800-228676200	Active TSS	HSMM	muscle
38	chr1:228673800-228676200	Active TSS	NHLF	lung
39	chr1:228673800-228676600	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:228673800-228676600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:228673800-228676800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:228674000-228674800	Active TSS	Stomach Mucosa	stomach
43	chr1:228674000-228675000	Active TSS	Fetal Heart	heart
44	chr1:228674000-228675400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:228674000-228675600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:228674000-228675800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:228674000-228675800	Active TSS	Primary hematopoietic stem cells	blood
48	chr1:228674000-228675800	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:228674000-228675800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr1:228674000-228675800	Active TSS	Brain Substantia Nigra	brain

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