Variant report

Variant	rs112671457
Chromosome Location	chr5:98108362-98108363
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	GATA2	chr5:98108248-98110520	SH-SY5Y	brain:	n/a	chr5:98109257-98109267
2	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
3	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
4	POLR2A	chr5:98107933-98109677	SK-N-SH	brain:	n/a	n/a
5	HCFC1	chr5:98108112-98110714	Hela-S3	cervix:	n/a	n/a
6	E2F6	chr5:98108284-98110633	A549	lung:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
7	KAP1	chr5:98107981-98109585	HEK293	kidney:	n/a	n/a
8	CTCF	chr5:98106325-98108512	SK-N-SH	brain:	n/a	chr5:98108010-98108017
9	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
10	POLR2A	chr5:98107747-98110006	U87	brain:	n/a	n/a
11	ZNF263	chr5:98107892-98110575	HEK293-T-REx	kidney:	n/a	chr5:98109086-98109107 chr5:98109255-98109264
12	MXI1	chr5:98107889-98112517	IMR90	lung:	n/a	n/a
13	REST	chr5:98108334-98110648	H1-neurons	neurons:	n/a	chr5:98109985-98109998
14	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
15	MYC	chr5:98108015-98108376	MCF10A-Er-Src	breast:	n/a	n/a
16	HA-E2F1	chr5:98108345-98110719	MCF-7	breast:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
17	POLR2A	chr5:98107741-98110666	U87	brain:	n/a	n/a
18	MXI1	chr5:98107942-98112468	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr5:98108220-98108370	GM12872	blood:	n/a	n/a
20	POLR2A	chr5:98107919-98110578	ProgFib	skin:	n/a	n/a
21	TCF7L2	chr5:98108356-98109248	HEK293	kidney:	n/a	n/a
22	MAX	chr5:98107978-98110797	A549	lung:	n/a	chr5:98109181-98109191
23	STAT1	chr5:98108217-98108593	GM12878	blood:	n/a	n/a
24	E2F6	chr5:98108255-98110734	H1-hESC	embryonic stem cell:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584

No.	Distal block	Cell Line	Cell type
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:
3	chr17:59476329..59477978-chr5:98107765..98110191,2	MCF-7	breast:
4	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1-1	chr5:98108326-98108502	ENSG00000246763.2
2	lnc-CHD1-1	chr5:98108326-98108792	ENSG00000246763.2
3	lnc-CHD1-1	chr5:98108326-98108482	ENSG00000246763.2
4	lnc-CHD1-1	chr5:98108326-98108456	NONHSAT102953
5	lnc-CHD1-1	chr5:98108326-98108419	NONHSAT102954
6	lnc-CHD1-1	chr5:98108326-98108788	NR_033932
7	lnc-CHD1-1	chr5:98108326-98108780	NONHSAT102949
8	lnc-CHD1-1	chr5:98108326-98108502	NONHSAT102950

Variant related genes	Relation type
RGMB	TF binding region
ENSG00000174136	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000251513	Chromatin interaction
ENSG00000058729	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3339628	chr5:98107452-98111750	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	esv3394593	chr5:98108277-98110825	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
3	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:98104200-98111600	Active TSS	Right Atrium	heart
5	chr5:98104400-98109800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
7	chr5:98104600-98108600	Active TSS	Fetal Stomach	stomach
8	chr5:98105200-98109400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:98106000-98108800	Weak transcription	Spleen	Spleen
10	chr5:98106400-98108600	Active TSS	Fetal Muscle Trunk	muscle
11	chr5:98106400-98108800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:98106400-98108800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:98106400-98108800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
14	chr5:98106400-98109400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:98106600-98108800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:98106600-98108800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:98107000-98108400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr5:98107000-98108400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:98107200-98108400	Weak transcription	Esophagus	oesophagus
20	chr5:98107200-98108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:98107200-98108600	Weak transcription	Small Intestine	intestine
22	chr5:98107400-98108400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:98107400-98108400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr5:98107400-98108400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
25	chr5:98107400-98108400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr5:98107400-98108400	Weak transcription	Ovary	ovary
27	chr5:98107400-98108400	Enhancers	Hela-S3	cervix
28	chr5:98107400-98108600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr5:98107400-98108600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:98107400-98108600	Weak transcription	Aorta	Aorta
31	chr5:98107400-98108600	Weak transcription	Left Ventricle	heart
32	chr5:98107400-98108800	Flanking Active TSS	HUVEC	blood vessel
33	chr5:98107400-98109600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:98107600-98108400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:98107600-98108400	Bivalent Enhancer	Primary B cells from cord blood	blood
36	chr5:98107600-98108400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:98107600-98108400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:98107600-98108400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:98107600-98108400	Enhancers	Adipose Nuclei	Adipose
40	chr5:98107600-98108600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
41	chr5:98107600-98108600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:98107600-98108800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:98107600-98108800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:98107600-98108800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr5:98107600-98108800	Flanking Active TSS	NH-A	brain
46	chr5:98107800-98108400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
47	chr5:98107800-98108400	Enhancers	Primary B cells from peripheral blood	blood
48	chr5:98107800-98108400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:98107800-98108400	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr5:98107800-98108400	Bivalent Enhancer	HepG2	liver

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