Variant report

Variant	rs12511417
Chromosome Location	chr4:8440951-8440952
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	MXI1	chr4:8440826-8443653	IMR90	lung:	n/a	n/a
2	FOXA2	chr4:8440942-8441258	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:8440524-8443902	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA1	chr4:8440881-8441235	T-47D	breast:	n/a	chr4:8441096-8441111
5	FOXA1	chr4:8440876-8441260	T-47D	breast:	n/a	chr4:8441096-8441111
6	MYC	chr4:8440829-8442644	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr4:8440925-8441216	T-47D	breast:	n/a	n/a
8	SETDB1	chr4:8440922-8442549	K562	blood:	n/a	n/a
9	EP300	chr4:8440900-8441249	T-47D	breast:	n/a	n/a
10	GATA3	chr4:8440899-8441283	T-47D	breast:	n/a	n/a
11	POLR2A	chr4:8440912-8442800	IMR90	lung:	n/a	n/a
12	FOXA1	chr4:8440856-8441290	HepG2	liver:	n/a	chr4:8441096-8441111
13	GATA3	chr4:8440901-8441219	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8428810..8430394-chr4:8440724..8444143,3	K562	blood:
2	chr4:8430205..8432229-chr4:8440824..8442595,2	MCF-7	breast:
3	chr4:8428067..8433323-chr4:8440948..8445760,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL19-2	chr4:8440519-8441028	NONHSAT095098

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000087008	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10003554	1.00[ASN][1000 genomes]
rs10516192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933361	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938744	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12108233	0.89[EUR][1000 genomes]
rs12108264	0.89[EUR][1000 genomes]
rs12108299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498220	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12498652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12498856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12499366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs12500106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500186	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501889	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503080	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12504328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12504813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506061	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12506272	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506429	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506703	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509044	1.00[ASN][1000 genomes]
rs12509545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511591	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512044	1.00[ASN][1000 genomes]
rs12513048	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12513296	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842315	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842316	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842333	1.00[CHB][hapmap]
rs2386224	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2386225	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34873641	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41264711	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55856487	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57229672	1.00[ASN][1000 genomes]
rs59670959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59872851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62286004	1.00[ASN][1000 genomes]
rs6447869	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs66675498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66794792	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67332046	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67496006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67901119	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813671	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814866	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830523	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs6849528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6855235	1.00[CHB][hapmap]
rs73209462	1.00[ASN][1000 genomes]
rs73209465	1.00[ASN][1000 genomes]
rs73209470	1.00[ASN][1000 genomes]
rs73209473	1.00[ASN][1000 genomes]
rs73209478	1.00[ASN][1000 genomes]
rs73209480	1.00[ASN][1000 genomes]
rs73209481	1.00[ASN][1000 genomes]
rs73209488	1.00[ASN][1000 genomes]
rs73209489	1.00[ASN][1000 genomes]
rs73209502	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73211306	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73211309	1.00[ASN][1000 genomes]
rs73211315	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211334	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73211338	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211340	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211347	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73211354	0.89[EUR][1000 genomes]
rs73211357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211359	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211366	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211368	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211375	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211381	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211383	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211388	1.00[EUR][1000 genomes]
rs73211394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211401	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213403	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213404	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213406	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213408	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213409	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213410	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213413	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213414	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213420	1.00[EUR][1000 genomes]
rs73213426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223246	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223256	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223257	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223259	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223263	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223271	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223275	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223282	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223294	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686550	1.00[ASN][1000 genomes]
rs9761200	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8430800-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:8430800-8441400	Weak transcription	Fetal Brain Female	brain
3	chr4:8430800-8441800	Weak transcription	Aorta	Aorta
4	chr4:8431000-8441000	Weak transcription	A549	lung
5	chr4:8431000-8441200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:8431000-8441600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:8433800-8442000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:8435600-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:8437800-8441000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:8437800-8441200	Enhancers	Liver	Liver
11	chr4:8437800-8441400	Weak transcription	HSMM	muscle
12	chr4:8438000-8441000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:8438000-8441400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:8438000-8441400	Weak transcription	NHDF-Ad	bronchial
15	chr4:8438000-8441800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:8438200-8441200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:8438200-8441200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:8438200-8441200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:8438200-8441400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:8438200-8441400	Weak transcription	Fetal Heart	heart
21	chr4:8438200-8441600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:8438200-8441600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:8438200-8441800	Weak transcription	Gastric	stomach
24	chr4:8438200-8442000	Weak transcription	Spleen	Spleen
25	chr4:8438400-8441000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:8438400-8441200	Weak transcription	Primary B cells from cord blood	blood
27	chr4:8438400-8442000	Weak transcription	Small Intestine	intestine
28	chr4:8439000-8441600	Enhancers	Brain Substantia Nigra	brain
29	chr4:8439000-8441800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:8439200-8441400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:8439200-8441400	Enhancers	Stomach Mucosa	stomach
32	chr4:8439400-8441200	Weak transcription	Brain Germinal Matrix	brain
33	chr4:8439400-8441400	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:8439400-8441400	Weak transcription	Fetal Brain Male	brain
35	chr4:8439400-8441600	Enhancers	Fetal Thymus	thymus
36	chr4:8439600-8441000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:8439600-8441000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:8439600-8441000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:8439600-8441000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:8439600-8441000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:8439600-8441200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:8439600-8441200	Enhancers	HMEC	breast
43	chr4:8439600-8441400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:8439600-8441400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:8439600-8441400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:8439600-8441400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:8439600-8441400	Enhancers	Brain Anterior Caudate	brain
48	chr4:8439600-8441400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr4:8439600-8441400	Weak transcription	Psoas Muscle	Psoas
50	chr4:8439600-8441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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