Variant report

Variant	rs2631729
Chromosome Location	chr4:8436249-8436250
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	ZNF263	chr4:8436092-8436268	HEK293-T-REx	kidney:	n/a	n/a
2	TEAD4	chr4:8436064-8436358	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:8434308-8436649	K562	blood:	n/a	n/a
4	POLR2A	chr4:8436175-8436306	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8432954..8436469-chr4:8440393..8443055,5	K562	blood:
2	chr4:8433688..8436302-chr4:8440393..8442354,2	K562	blood:
3	chr4:8433605..8436324-chr4:8439088..8441322,2	MCF-7	breast:
4	chr4:8429167..8433207-chr4:8433579..8437549,5	K562	blood:
5	chr4:8217481..8219669-chr4:8436164..8438381,2	MCF-7	breast:

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000155275	Chromatin interaction
ENSG00000087008	Chromatin interaction
ENSG00000125089	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11729265	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12503034	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880025	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002860	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049302	0.95[ASN][1000 genomes]
rs2140336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2245515	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245808	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245809	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2386223	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631723	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631724	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631727	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631728	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631730	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631733	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631737	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631750	0.81[ASN][1000 genomes]
rs2631752	0.89[ASN][1000 genomes]
rs2631757	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631763	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2631764	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631765	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2631766	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631767	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631769	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688221	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688228	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688229	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688234	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688239	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688240	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688244	0.98[ASN][1000 genomes]
rs2688246	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103090	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3103098	0.86[JPT][hapmap]
rs3115396	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3775893	0.87[EUR][1000 genomes]
rs4325994	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56343159	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954270	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs954271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8430600-8436600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:8430600-8437200	Weak transcription	HSMM	muscle
3	chr4:8430800-8436400	Weak transcription	Primary T cells from cord blood	blood
4	chr4:8430800-8436600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:8430800-8437000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:8430800-8437200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:8430800-8437200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:8430800-8437400	Weak transcription	Left Ventricle	heart
9	chr4:8430800-8437400	Weak transcription	Psoas Muscle	Psoas
10	chr4:8430800-8437600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:8430800-8439000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:8430800-8439000	Weak transcription	Brain Germinal Matrix	brain
13	chr4:8430800-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:8430800-8441400	Weak transcription	Fetal Brain Female	brain
15	chr4:8430800-8441800	Weak transcription	Aorta	Aorta
16	chr4:8431000-8436400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:8431000-8436400	Weak transcription	Thymus	Thymus
18	chr4:8431000-8436600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:8431000-8436600	Weak transcription	Primary B cells from cord blood	blood
20	chr4:8431000-8436600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:8431000-8436600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:8431000-8436600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:8431000-8436600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:8431000-8436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:8431000-8436800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:8431000-8437200	Weak transcription	Adipose Nuclei	Adipose
27	chr4:8431000-8437200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:8431000-8437200	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:8431000-8437200	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:8431000-8437200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:8431000-8437200	Weak transcription	K562	blood
32	chr4:8431000-8437400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:8431000-8437400	Weak transcription	Fetal Heart	heart
34	chr4:8431000-8437400	Weak transcription	Right Ventricle	heart
35	chr4:8431000-8437400	Weak transcription	HUVEC	blood vessel
36	chr4:8431000-8437400	Weak transcription	NHLF	lung
37	chr4:8431000-8437400	Weak transcription	Osteobl	bone
38	chr4:8431000-8437600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:8431000-8437600	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:8431000-8437600	Weak transcription	Brain Substantia Nigra	brain
41	chr4:8431000-8439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:8431000-8439000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:8431000-8439200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:8431000-8439200	Weak transcription	Brain Angular Gyrus	brain
45	chr4:8431000-8439200	Weak transcription	Fetal Brain Male	brain
46	chr4:8431000-8440600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:8431000-8441000	Weak transcription	A549	lung
48	chr4:8431000-8441200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:8431000-8441600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:8431800-8437200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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