Variant report

Variant	rs74140956
Chromosome Location	chr1:228282275-228282276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228282169-228282427	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228282142-228282492	GM12891	blood:	n/a	n/a
4	TCF12	chr1:228282100-228282700	A549	lung:	n/a	n/a
5	POLR2A	chr1:228282090-228282454	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:228281522-228282637	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:228282066-228282529	K562	blood:	n/a	n/a
8	POLR2A	chr1:228281517-228282740	SK-N-MC	brain:	n/a	n/a
9	TRIM28	chr1:228282267-228282694	K562	blood:	n/a	n/a
10	POLR2A	chr1:228281688-228282423	GM12878	blood:	n/a	n/a
11	CBX3	chr1:228281725-228282732	K562	blood:	n/a	n/a
12	POLR2A	chr1:228281597-228282425	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:228282013-228282426	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
15	KAP1	chr1:228281869-228282834	K562	blood:	n/a	n/a
16	POLR2A	chr1:228282168-228282419	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:228279745-228282720	K562	blood:	n/a	n/a
18	POLR2A	chr1:228281686-228283098	Hela-S3	cervix:	n/a	n/a
19	CBX3	chr1:228282225-228282681	K562	blood:	n/a	n/a
20	POLR2A	chr1:228279806-228282603	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:228281416-228282696	K562	blood:	n/a	n/a
22	ELF1	chr1:228282193-228282433	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
24	KAP1	chr1:228281807-228282875	HEK293	kidney:	n/a	chr1:228282846-228282854
25	POLR2A	chr1:228282216-228282719	K562	blood:	n/a	n/a
26	POLR2A	chr1:228281659-228282699	PFSK-1	brain:	n/a	n/a
27	CEBPB	chr1:228282182-228282654	K562	blood:	n/a	n/a
28	POLR2A	chr1:228281613-228282588	GM12891	blood:	n/a	n/a
29	POLR2A	chr1:228281807-228282819	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:228281554-228282541	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:228281557-228282586	HL-60	blood:	n/a	n/a
32	POLR2A	chr1:228282261-228282301	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:228282124-228282694	K562	blood:	n/a	n/a
34	POLR2A	chr1:228281665-228282637	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228281021..228283258-chr1:228327400..228329608,2	MCF-7	breast:
2	chr1:228281446..228284269-chr1:228337109..228339071,2	K562	blood:
3	chr1:228282033..228284613-chr1:228342310..228344410,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000143774	Chromatin interaction
ENSG00000198835	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10127654	1.00[AMR][1000 genomes]
rs11541554	1.00[AMR][1000 genomes]
rs15109	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16848270	1.00[ASN][1000 genomes]
rs2231717	1.00[AMR][1000 genomes]
rs3754359	0.92[AFR][1000 genomes]
rs55662277	1.00[AMR][1000 genomes]
rs55686465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55904630	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55923168	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56003736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56029925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56080014	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56137152	1.00[AMR][1000 genomes]
rs56280722	1.00[AMR][1000 genomes]
rs56285667	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56377909	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56386805	1.00[AMR][1000 genomes]
rs56410225	1.00[AMR][1000 genomes]
rs56831205	1.00[ASN][1000 genomes]
rs57446195	1.00[ASN][1000 genomes]
rs58045861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59460700	1.00[AMR][1000 genomes]
rs59478442	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60245137	1.00[ASN][1000 genomes]
rs60628313	1.00[AMR][1000 genomes]
rs61100243	1.00[AMR][1000 genomes]
rs61230585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61401568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61737797	1.00[ASN][1000 genomes]
rs74140905	0.92[AFR][1000 genomes]
rs74140907	1.00[ASN][1000 genomes]
rs74140910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140912	1.00[ASN][1000 genomes]
rs74140915	1.00[ASN][1000 genomes]
rs74140916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140918	1.00[ASN][1000 genomes]
rs74140919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140925	1.00[ASN][1000 genomes]
rs74140953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140960	1.00[ASN][1000 genomes]
rs74140961	1.00[ASN][1000 genomes]
rs74140962	0.92[AFR][1000 genomes]
rs74140963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140965	1.00[ASN][1000 genomes]
rs74140967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140968	0.92[AFR][1000 genomes]
rs74140969	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140970	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140973	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140974	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140975	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140976	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140977	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140981	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140985	0.85[AFR][1000 genomes]
rs74140986	1.00[AMR][1000 genomes]
rs74140987	1.00[AMR][1000 genomes]
rs74140988	1.00[AMR][1000 genomes]
rs74140989	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140990	1.00[AMR][1000 genomes]
rs74140994	0.90[ASN][1000 genomes]
rs74140996	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140999	1.00[AMR][1000 genomes]
rs74141000	1.00[AMR][1000 genomes]
rs74141002	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142604	1.00[AMR][1000 genomes]
rs74142605	1.00[AMR][1000 genomes]
rs74142606	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142608	0.90[ASN][1000 genomes]
rs74142610	1.00[AMR][1000 genomes]
rs74142611	1.00[AMR][1000 genomes]
rs74142613	1.00[AMR][1000 genomes]
rs74142618	1.00[AMR][1000 genomes]
rs74142619	1.00[AMR][1000 genomes]
rs74142622	1.00[AMR][1000 genomes]
rs74142625	0.90[ASN][1000 genomes]
rs74142626	1.00[AMR][1000 genomes]
rs74142627	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142629	1.00[AMR][1000 genomes]
rs74142630	1.00[AMR][1000 genomes]
rs74142642	0.90[ASN][1000 genomes]
rs74142644	0.90[ASN][1000 genomes]
rs74142645	0.90[ASN][1000 genomes]
rs74142647	0.90[ASN][1000 genomes]
rs74143631	1.00[ASN][1000 genomes]
rs74143632	1.00[ASN][1000 genomes]
rs74143634	1.00[ASN][1000 genomes]
rs74143635	1.00[ASN][1000 genomes]
rs74143636	1.00[ASN][1000 genomes]
rs74143637	1.00[ASN][1000 genomes]
rs74143638	1.00[ASN][1000 genomes]
rs74143640	1.00[ASN][1000 genomes]
rs74143641	1.00[ASN][1000 genomes]
rs74143642	1.00[ASN][1000 genomes]
rs74143662	1.00[ASN][1000 genomes]
rs74143665	1.00[ASN][1000 genomes]
rs74143667	1.00[ASN][1000 genomes]
rs752108	1.00[ASN][1000 genomes]
rs752109	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	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
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	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
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
5	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
10	chr1:228278800-228282800	ZNF genes & repeats	GM12878-XiMat	blood
11	chr1:228278800-228283000	ZNF genes & repeats	Dnd41	blood
12	chr1:228278800-228283600	Weak transcription	Ovary	ovary
13	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
14	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:228279400-228283400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:228279400-228284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:228279600-228285600	Weak transcription	NH-A	brain
18	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr1:228279800-228282600	ZNF genes & repeats	K562	blood
20	chr1:228280000-228283600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:228280000-228283600	ZNF genes & repeats	Thymus	Thymus
22	chr1:228280000-228284000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:228280000-228284000	ZNF genes & repeats	Fetal Thymus	thymus
24	chr1:228280000-228284200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach
26	chr1:228280200-228282800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:228280200-228282800	ZNF genes & repeats	HepG2	liver
28	chr1:228280200-228283200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr1:228280200-228283400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr1:228280200-228284400	ZNF genes & repeats	Fetal Brain Female	brain
31	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
32	chr1:228280400-228283400	ZNF genes & repeats	A549	lung
33	chr1:228280400-228283600	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr1:228280400-228285400	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr1:228280600-228282800	Strong transcription	Osteobl	bone
36	chr1:228280600-228283800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:228280600-228286400	Weak transcription	Psoas Muscle	Psoas
38	chr1:228280800-228282400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:228280800-228282800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr1:228280800-228283400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
42	chr1:228281000-228282400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:228281000-228283000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:228281000-228283200	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr1:228281000-228283400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
46	chr1:228281000-228283400	ZNF genes & repeats	NHLF	lung
47	chr1:228281000-228283600	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr1:228281000-228284000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:228281200-228282400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:228281200-228283200	Weak transcription	Gastric	stomach

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