Variant report

Variant	rs41277656
Chromosome Location	chr13:95366207-95366208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr13:95363903-95366238	H1-hESC	embryonic stem cell:	n/a	chr13:95364649-95364660 chr13:95364957-95364966
2	MAX	chr13:95363043-95366255	H1-hESC	embryonic stem cell:	n/a	chr13:95364328-95364338 chr13:95365842-95365852 chr13:95364441-95364451
3	MAX	chr13:95365807-95366232	H1-hESC	embryonic stem cell:	n/a	chr13:95365842-95365852
4	ZNF263	chr13:95363302-95366442	HEK293-T-REx	kidney:	n/a	chr13:95365861-95365870 chr13:95364830-95364851 chr13:95365858-95365867 chr13:95364868-95364889 chr13:95364662-95364671 chr13:95365767-95365776
5	GTF2F1	chr13:95366143-95366235	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr13:95363183-95366208	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:95366203-95366253	NB4	blood:	n/a
2	chr13:95366203-95366253	K562	blood:	n/a
3	chr13:95366203-95366253	A549	lung:	n/a
4	chr13:95366203-95366253	HAEpiC	amniotic membrane:	n/a
5	chr13:95366203-95366253	HEK293	kidney:	embryo
6	chr13:95366203-95366253	NHBE	bronchial:	n/a
7	chr13:95366203-95366253	PFSK-1	brain:	n/a
8	chr13:95366203-95366253	IMR90	lung:	fetal
9	chr13:95366203-95366253	Hepatocyte	liver:	n/a
10	chr13:95366203-95366253	GM19239	blood:	n/a
11	chr13:95366203-95366253	ProgFib	skin:	n/a
12	chr13:95366203-95366253	MCF10A-Er-Src	breast:	n/a
13	chr13:95366203-95366253	GM12892	blood:	n/a
14	chr13:95366203-95366253	HCPEpiC	choroid plexus:	n/a
15	chr13:95366203-95366253	HNPCEpiC	eye:	n/a
16	chr13:95366203-95366253	AG04450	lung:	fetal
17	chr13:95366203-95366253	LNCaP	prostate:	n/a
18	chr13:95366203-95366253	Hela-S3	cervix:	n/a
19	chr13:95366203-95366253	HepG2	liver:	n/a
20	chr13:95366203-95366253	HMEC	breast:	n/a
21	chr13:95366203-95366253	T-47D	breast:	n/a
22	chr13:95366203-95366253	HUVEC	blood vessel:	n/a
23	chr13:95366203-95366253	SKMC	muscle:	n/a
24	chr13:95366203-95366253	Jurkat	blood:	n/a
25	chr13:95366203-95366253	HRPEpiC	eye:	n/a
26	chr13:95366203-95366253	GM06990	blood:	n/a
27	chr13:95366203-95366253	HCM	heart:	n/a
28	chr13:95366203-95366253	HL-60	blood:	n/a
29	chr13:95366203-95366253	AG04449	skin:	fetal
30	chr13:95366203-95366253	HPAEpiC	pulmonary alveolar:	n/a
31	chr13:95366203-95366253	U87	brain:	n/a
32	chr13:95366203-95366253	H1-hESC	embryonic stem cell:	embryo
33	chr13:95366203-95366253	BE2_C	brain:	n/a
34	chr13:95366203-95366253	SK-N-SH_RA	brain:	n/a
35	chr13:95366203-95366253	CMK	blood:	n/a
36	chr13:95366203-95366253	AG09319	gingival:	n/a
37	chr13:95366203-95366253	NH-A	brain:	n/a
38	chr13:95366203-95366253	HCT-116	colon:	n/a
39	chr13:95366203-95366253	HIPEpiC	eye:	n/a
40	chr13:95366203-95366253	ECC-1	luminal epithelium:	n/a
41	chr13:95366203-95366253	Caco-2	colon:	n/a
42	chr13:95366203-95366253	AoSMC	blood vessel:	n/a
43	chr13:95366203-95366253	NHDF-neo	bronchial:	n/a
44	chr13:95366203-95366253	HEEpiC	esophagus:	n/a
45	chr13:95366203-95366253	NT2-D1	testis:	n/a
46	chr13:95366203-95366253	HRCEpiC	kidney:	n/a
47	chr13:95366203-95366253	GM12891	blood:	n/a
48	chr13:95366203-95366253	SK-N-MC	brain:	n/a
49	chr13:95366203-95366253	AG09309	skin:	n/a
50	chr13:95366203-95366253	MCF-7	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95359884..95364398-chr13:95364758..95367708,4	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR180-1	chr13:95365892-95368197	XLOC_010472
2	lnc-GPR180-1	chr13:95365892-95368199	NR_046514
3	lnc-GPR180-1	chr13:95365892-95368500	ENSG00000227640.2

No data

Variant related genes	Relation type
SOX21	TF binding region
SOX21	CpG island
ENSG00000125285	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1830863	1.00[AFR][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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv1813549	chr13:95333331-95377127	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv826750	chr13:95358502-95368070	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1054343	chr13:95362727-95395486	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3446235	chr13:95362851-95366749	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95359000-95368000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:95359200-95366600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:95359600-95366400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:95362400-95366600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr13:95362400-95366800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
6	chr13:95362600-95366400	Active TSS	Brain Substantia Nigra	brain
7	chr13:95362800-95366400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
8	chr13:95362800-95366800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr13:95363000-95366400	Bivalent/Poised TSS	NHEK	skin
10	chr13:95363000-95366600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr13:95363400-95366400	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr13:95363600-95367000	Active TSS	Brain Anterior Caudate	brain
13	chr13:95363600-95367800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:95364400-95366400	Bivalent Enhancer	Fetal Brain Male	brain
15	chr13:95364600-95366400	Active TSS	Gastric	stomach
16	chr13:95364800-95366400	Active TSS	Esophagus	oesophagus
17	chr13:95365200-95366400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:95365200-95366400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:95365200-95366800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:95365800-95366600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:95365800-95366600	Bivalent/Poised TSS	Fetal Stomach	stomach
22	chr13:95365800-95366800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:95365800-95366800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr13:95366000-95366400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:95366000-95366600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr13:95366000-95366800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr13:95366000-95367000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr13:95366200-95366400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr13:95366200-95366400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
30	chr13:95366200-95366400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:95366200-95366400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr13:95366200-95366400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
33	chr13:95366200-95366400	Bivalent Enhancer	NH-A	brain
34	chr13:95366200-95366600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr13:95366200-95366600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:95366200-95366800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
37	chr13:95366200-95366800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr13:95366200-95366800	Active TSS	Brain Germinal Matrix	brain
39	chr13:95366200-95367200	Active TSS	Stomach Mucosa	stomach

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