Variant report

Variant	rs2688246
Chromosome Location	chr4:8441264-8441265
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	JUN	chr4:8440970-8443464	K562	blood:	n/a	chr4:8442293-8442304 chr4:8442412-8442426
2	MXI1	chr4:8440826-8443653	IMR90	lung:	n/a	n/a
3	STAT3	chr4:8440953-8441440	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:8440524-8443902	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr4:8440829-8442644	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr4:8441064-8442724	MCF10A-Er-Src	breast:	n/a	n/a
7	SETDB1	chr4:8440922-8442549	K562	blood:	n/a	n/a
8	GATA3	chr4:8440899-8441283	T-47D	breast:	n/a	n/a
9	MXI1	chr4:8441003-8443406	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr4:8440912-8442800	IMR90	lung:	n/a	n/a
11	FOXA1	chr4:8440856-8441290	HepG2	liver:	n/a	chr4:8441096-8441111
12	TBP	chr4:8440995-8441457	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:8440963-8443196	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr4:8441206-8442776	GM12891	blood:	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:

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

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11729265	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503034	0.89[ASN][1000 genomes]
rs1880025	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002860	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2049302	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2140336	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2245515	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245808	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245809	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2386223	0.90[ASN][1000 genomes]
rs2631723	0.81[ASN][1000 genomes]
rs2631727	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631728	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2631729	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631730	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631733	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631737	0.93[ASN][1000 genomes]
rs2631752	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631757	0.87[ASN][1000 genomes]
rs2631763	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631764	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631765	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2631766	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631767	0.92[ASN][1000 genomes]
rs2631769	0.93[ASN][1000 genomes]
rs2688221	0.93[ASN][1000 genomes]
rs2688228	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688229	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688230	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688234	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688239	0.81[ASN][1000 genomes]
rs2688244	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3103090	0.85[ASN][1000 genomes]
rs4325994	0.87[ASN][1000 genomes]
rs56343159	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954270	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954271	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8430800-8441400	Weak transcription	Fetal Brain Female	brain
2	chr4:8430800-8441800	Weak transcription	Aorta	Aorta
3	chr4:8431000-8441600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:8433800-8442000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:8437800-8441400	Weak transcription	HSMM	muscle
6	chr4:8438000-8441400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr4:8438000-8441400	Weak transcription	NHDF-Ad	bronchial
8	chr4:8438000-8441800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:8438200-8441400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:8438200-8441400	Weak transcription	Fetal Heart	heart
11	chr4:8438200-8441600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:8438200-8441600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:8438200-8441800	Weak transcription	Gastric	stomach
14	chr4:8438200-8442000	Weak transcription	Spleen	Spleen
15	chr4:8438400-8442000	Weak transcription	Small Intestine	intestine
16	chr4:8439000-8441600	Enhancers	Brain Substantia Nigra	brain
17	chr4:8439000-8441800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:8439200-8441400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr4:8439200-8441400	Enhancers	Stomach Mucosa	stomach
20	chr4:8439400-8441400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:8439400-8441400	Weak transcription	Fetal Brain Male	brain
22	chr4:8439400-8441600	Enhancers	Fetal Thymus	thymus
23	chr4:8439600-8441400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:8439600-8441400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:8439600-8441400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:8439600-8441400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:8439600-8441400	Enhancers	Brain Anterior Caudate	brain
28	chr4:8439600-8441400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:8439600-8441400	Weak transcription	Psoas Muscle	Psoas
30	chr4:8439600-8441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:8439600-8441600	Enhancers	Fetal Intestine Small	intestine
32	chr4:8439600-8441600	Weak transcription	Right Atrium	heart
33	chr4:8439600-8441800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:8439600-8441800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:8439600-8441800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:8439600-8441800	Weak transcription	Esophagus	oesophagus
37	chr4:8439600-8441800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:8439600-8441800	Weak transcription	Left Ventricle	heart
39	chr4:8439600-8441800	Weak transcription	Lung	lung
40	chr4:8439600-8441800	Weak transcription	Pancreas	Pancrea
41	chr4:8439600-8442000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:8439600-8442000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:8439600-8442000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:8439600-8443800	Active TSS	K562	blood
45	chr4:8439800-8441400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:8439800-8441400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:8439800-8441400	Weak transcription	HSMMtube	muscle
48	chr4:8439800-8441600	Enhancers	Fetal Lung	lung
49	chr4:8439800-8441800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:8439800-8441800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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