Variant report

Variant	rs527339529
Chromosome Location	chr5:98108483-98108484
allele	A/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	GABPA	chr5:98108477-98109459	MCF-7	breast:	n/a	chr5:98109181-98109190
3	SIN3AK20	chr5:98108444-98108812	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr5:98108409-98110611	A549	lung:	n/a	chr5:98110256-98110265
5	MAX	chr5:98108437-98110865	HepG2	liver:	n/a	chr5:98109181-98109191
6	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
7	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
8	POLR2A	chr5:98108473-98109656	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr5:98107933-98109677	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr5:98108421-98110443	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr5:98108408-98109836	HUVEC	blood vessel:	n/a	n/a
12	HCFC1	chr5:98108112-98110714	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr5:98108284-98110633	A549	lung:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
14	MYC	chr5:98108396-98110663	A549	lung:	n/a	chr5:98109181-98109191
15	SP1	chr5:98108437-98109820	HCT-116	colon:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
16	POLR2A	chr5:98108439-98110648	H1-hESC	embryonic stem cell:	n/a	n/a
17	KAP1	chr5:98107981-98109585	HEK293	kidney:	n/a	n/a
18	CTCF	chr5:98106325-98108512	SK-N-SH	brain:	n/a	chr5:98108010-98108017
19	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
20	POLR2A	chr5:98108465-98110670	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr5:98107747-98110006	U87	brain:	n/a	n/a
22	ZNF263	chr5:98107892-98110575	HEK293-T-REx	kidney:	n/a	chr5:98109086-98109107 chr5:98109255-98109264
23	MAX	chr5:98108478-98110741	MCF-7	breast:	n/a	chr5:98109181-98109191
24	MAX	chr5:98108471-98110770	HepG2	liver:	n/a	chr5:98109181-98109191
25	MXI1	chr5:98107889-98112517	IMR90	lung:	n/a	n/a
26	SP1	chr5:98108479-98109669	A549	lung:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
27	SIN3A	chr5:98108392-98111565	H1-hESC	embryonic stem cell:	n/a	chr5:98109597-98109608 chr5:98109985-98109998 chr5:98110167-98110180
28	REST	chr5:98108334-98110648	H1-neurons	neurons:	n/a	chr5:98109985-98109998
29	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
30	MAX	chr5:98108435-98110742	ECC-1	luminal epithelium:	n/a	chr5:98109181-98109191
31	SIN3AK20	chr5:98108443-98109613	MCF-7	breast:	n/a	n/a
32	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
33	MAX	chr5:98108378-98110189	HCT-116	colon:	n/a	chr5:98109181-98109191
34	MXI1	chr5:98108442-98110955	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr5:98107741-98110666	U87	brain:	n/a	n/a
36	MXI1	chr5:98107942-98112468	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr5:98108479-98109702	SK-N-MC	brain:	n/a	n/a
38	SP1	chr5:98108473-98109816	HCT-116	colon:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
39	POLR2A	chr5:98107919-98110578	ProgFib	skin:	n/a	n/a
40	MAX	chr5:98108459-98110795	H1-hESC	embryonic stem cell:	n/a	chr5:98109181-98109191
41	EP300	chr5:98108483-98110464	SK-N-SH	brain:	n/a	chr5:98110094-98110110 chr5:98110094-98110103 chr5:98109562-98109578 chr5:98109535-98109551 chr5:98108853-98108869 chr5:98109594-98109610
42	TCF7L2	chr5:98108356-98109248	HEK293	kidney:	n/a	n/a
43	MAX	chr5:98107978-98110797	A549	lung:	n/a	chr5:98109181-98109191
44	STAT1	chr5:98108217-98108593	GM12878	blood:	n/a	n/a
45	MAX	chr5:98108445-98110634	A549	lung:	n/a	chr5:98109181-98109191
46	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	chr5:98108326-98108788	NR_033932
4	lnc-CHD1-1	chr5:98108326-98108780	NONHSAT102949
5	lnc-CHD1-1	chr5:98108326-98108502	NONHSAT102950

Variant related genes	Relation type
RGMB	TF binding region
RGMB-AS1	TF binding region
ENSG00000267131	Chromatin interaction
ENSG00000174136	Chromatin interaction
ENSG00000251513	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	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:122 , 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	chr5:98107200-98108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:98107200-98108600	Weak transcription	Small Intestine	intestine
19	chr5:98107400-98108600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:98107400-98108600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:98107400-98108600	Weak transcription	Aorta	Aorta
22	chr5:98107400-98108600	Weak transcription	Left Ventricle	heart
23	chr5:98107400-98108800	Flanking Active TSS	HUVEC	blood vessel
24	chr5:98107400-98109600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:98107600-98108600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr5:98107600-98108600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:98107600-98108800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:98107600-98108800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:98107600-98108800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr5:98107600-98108800	Flanking Active TSS	NH-A	brain
31	chr5:98107800-98108600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:98107800-98108600	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr5:98107800-98108800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:98107800-98108800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr5:98107800-98108800	Flanking Active TSS	NHEK	skin
36	chr5:98108000-98108600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
37	chr5:98108000-98108600	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr5:98108000-98108600	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr5:98108000-98108600	Flanking Active TSS	Fetal Brain Female	brain
40	chr5:98108000-98108600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr5:98108000-98108800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr5:98108000-98108800	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr5:98108000-98108800	Flanking Active TSS	Stomach Mucosa	stomach
44	chr5:98108000-98108800	Flanking Active TSS	HMEC	breast
45	chr5:98108200-98108600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:98108200-98108600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:98108200-98108600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:98108200-98108600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr5:98108200-98108600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr5:98108200-98108600	Flanking Active TSS	Fetal Heart	heart

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