Variant report

Variant	rs29001339
Chromosome Location	chr4:100010956-100010957
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr4:100010869-100011377	K562	blood:	n/a	chr4:100010940-100010961 chr4:100011087-100011102 chr4:100010947-100010958
2	HA-E2F1	chr4:100009119-100010991	MCF-7	breast:	n/a	chr4:100009757-100009766
3	STAT3	chr4:100010777-100010969	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:100010775-100011194	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:100010889-100011230	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr4:100010783-100011162	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr4:100010810-100011450	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:100009386-100011182	K562	blood:	n/a	n/a
9	MYC	chr4:100009292-100011454	K562	blood:	n/a	n/a
10	BHLHE40	chr4:100009166-100011411	K562	blood:	n/a	n/a
11	GATA2	chr4:100010594-100011289	SH-SY5Y	brain:	n/a	n/a
12	POLR2A	chr4:100010647-100011109	HepG2	liver:	n/a	n/a
13	MXI1	chr4:100008557-100011869	IMR90	lung:	n/a	n/a
14	POLR2A	chr4:100009307-100011204	K562	blood:	n/a	n/a
15	POLR2A	chr4:100009295-100011109	HepG2	liver:	n/a	n/a
16	FOS	chr4:100010816-100010956	MCF10A-Er-Src	breast:	n/a	n/a
17	TBP	chr4:100010738-100011399	K562	blood:	n/a	n/a
18	POLR2A	chr4:100009092-100011459	K562	blood:	n/a	n/a
19	HEY1	chr4:100009494-100011541	K562	blood:	n/a	n/a
20	HEY1	chr4:100010619-100011127	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:100009206-100011120	K562	blood:	n/a	n/a
22	POLR2A	chr4:100009295-100011021	K562	blood:	n/a	n/a
23	POLR2A	chr4:100010927-100011140	HepG2	liver:	n/a	n/a
24	POLR2A	chr4:100009268-100011370	K562	blood:	n/a	n/a
25	JUND	chr4:100010853-100011309	K562	blood:	n/a	n/a
26	FOS	chr4:100010756-100011192	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr4:100010788-100011322	MCF10A-Er-Src	breast:	n/a	n/a
28	MYC	chr4:100010842-100011113	MCF10A-Er-Src	breast:	n/a	n/a
29	HEY1	chr4:100010877-100011431	HepG2	liver:	n/a	n/a
30	MEF2A	chr4:100010878-100011276	K562	blood:	n/a	chr4:100010940-100010961 chr4:100011087-100011102 chr4:100010947-100010958
31	STAT3	chr4:100010797-100011297	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr4:100010636-100011453	K562	blood:	n/a	n/a
33	RCOR1	chr4:100010909-100011468	K562	blood:	n/a	n/a
34	EP300	chr4:100010895-100011392	K562	blood:	n/a	n/a
35	HEY1	chr4:100010808-100011130	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100008381..100011330-chr4:100056699..100058939,2	MCF-7	breast:
2	chr4:99955536..99957055-chr4:100010118..100011890,2	K562	blood:
3	chr4:100010805..100012670-chr4:100870311..100872681,2	K562	blood:
4	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
5	chr4:100010072..100012637-chr4:100483853..100485997,3	K562	blood:
6	chr4:99915328..99918402-chr4:100008331..100011431,5	MCF-7	breast:
7	chr4:100010297..100012013-chr4:100018638..100021523,2	K562	blood:
8	chr4:100010287..100011807-chr4:100330778..100333619,2	MCF-7	breast:
9	chr4:100008800..100012914-chr4:100866380..100869813,4	K562	blood:
10	chr4:99848192..99852255-chr4:100007586..100012546,7	K562	blood:
11	chr4:99849574..99853806-chr4:100008192..100011466,4	MCF-7	breast:
12	chr4:100008800..100013313-chr4:100866380..100869813,5	K562	blood:

No data

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000164031	Chromatin interaction
ENSG00000138823	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000198099	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000272777	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17028473	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028834	1.00[AMR][1000 genomes]
rs28364319	1.00[AMR][1000 genomes]
rs28730571	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730610	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs29001631	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55820222	1.00[AMR][1000 genomes]
rs59728850	1.00[AMR][1000 genomes]
rs6532799	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6828819	1.00[AMR][1000 genomes]
rs6831854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835771	1.00[AMR][1000 genomes]
rs72897134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72901271	1.00[AMR][1000 genomes]
rs72901287	1.00[AMR][1000 genomes]
rs72901294	1.00[AMR][1000 genomes]
rs72901295	1.00[AMR][1000 genomes]
rs7664906	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684674	1.00[AMR][1000 genomes]
rs7689911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1849572	chr4:100007243-100024396	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100006600-100011400	Active TSS	Colonic Mucosa	Colon
2	chr4:100006600-100012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:100006800-100012400	Active TSS	NHLF	lung
4	chr4:100007000-100011600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:100007000-100011600	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:100007200-100011000	Active TSS	Fetal Intestine Small	intestine
7	chr4:100007400-100012400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr4:100007400-100012600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:100007600-100011800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:100007600-100012200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:100007800-100011000	Active TSS	A549	lung
12	chr4:100007800-100011200	Active TSS	Muscle Satellite Cultured Cells	--
13	chr4:100007800-100012200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:100007800-100013400	Active TSS	K562	blood
15	chr4:100008000-100012400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:100008200-100011000	Active TSS	HSMM	muscle
17	chr4:100008200-100011400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr4:100008200-100011400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:100008200-100011400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:100008200-100011600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:100008200-100011600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:100008400-100011000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr4:100008400-100011000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:100008400-100011200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:100008400-100011200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:100008400-100011200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:100008400-100011600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr4:100008400-100011600	Active TSS	NHDF-Ad	bronchial
29	chr4:100008400-100011800	Active TSS	NHEK	skin
30	chr4:100008400-100012200	Active TSS	Brain Germinal Matrix	brain
31	chr4:100008400-100012400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:100008400-100012400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:100008600-100011000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:100008600-100011000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:100008600-100011000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:100008600-100011000	Active TSS	Fetal Intestine Large	intestine
37	chr4:100008600-100011400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:100008600-100011400	Active TSS	Fetal Kidney	kidney
39	chr4:100008600-100011400	Active TSS	GM12878-XiMat	blood
40	chr4:100008600-100011800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:100008600-100012000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:100008600-100012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr4:100008600-100012200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:100008600-100012800	Active TSS	Ovary	ovary
45	chr4:100008800-100011000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:100008800-100011000	Active TSS	Stomach Mucosa	stomach
47	chr4:100008800-100011200	Active TSS	Fetal Stomach	stomach
48	chr4:100008800-100011200	Bivalent/Poised TSS	HepG2	liver
49	chr4:100008800-100011400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:100008800-100011400	Active TSS	Psoas Muscle	Psoas

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