Variant report

Variant	rs3802299
Chromosome Location	chr8:3142086-3142087
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	RAD21	chr8:3142080-3142408	ECC-1	luminal epithelium:	n/a	chr8:3142280-3142299
2	CTCF	chr8:3141975-3142420	K562	blood:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
3	RAD21	chr8:3141392-3142549	H1-hESC	embryonic stem cell:	n/a	chr8:3142280-3142299
4	SIN3A	chr8:3142035-3142437	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr8:3142045-3142452	HepG2	liver:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
6	SMC3	chr8:3141973-3142498	GM12878	blood:	n/a	chr8:3142281-3142295
7	CTCF	chr8:3142059-3142398	H1-hESC	embryonic stem cell:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
8	RAD21	chr8:3142045-3142441	H1-hESC	embryonic stem cell:	n/a	chr8:3142280-3142299
9	RAD21	chr8:3141444-3142532	H1-hESC	embryonic stem cell:	n/a	chr8:3142280-3142299
10	RAD21	chr8:3142047-3142520	ECC-1	luminal epithelium:	n/a	chr8:3142280-3142299
11	SMC3	chr8:3142029-3142783	SK-N-SH	brain:	n/a	chr8:3142281-3142295
12	CTCF	chr8:3141908-3142653	A549	lung:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
13	CTCF	chr8:3141494-3142489	K562	blood:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
14	CTCF	chr8:3142071-3142430	H1-hESC	embryonic stem cell:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
15	RAD21	chr8:3142083-3142521	HepG2	liver:	n/a	chr8:3142280-3142299
16	MAZ	chr8:3142057-3142454	GM12878	blood:	n/a	n/a
17	RAD21	chr8:3142036-3142492	A549	lung:	n/a	chr8:3142280-3142299
18	CHD2	chr8:3142082-3142314	GM12878	blood:	n/a	n/a
19	CTCF	chr8:3141371-3142634	SK-N-SH	brain:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
20	RAD21	chr8:3141989-3142529	A549	lung:	n/a	chr8:3142280-3142299
21	CTCF	chr8:3141491-3142480	GM12878	blood:	n/a	chr8:3142281-3142302 chr8:3142279-3142297
22	RCOR1	chr8:3141959-3142327	K562	blood:	n/a	n/a
23	KAP1	chr8:3141354-3142369	U2OS	brain:	n/a	n/a
24	RAD21	chr8:3141546-3142651	SK-N-SH	brain:	n/a	chr8:3142280-3142299

Variant related genes	Relation type
CSMD1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11985163	1.00[JPT][hapmap]
rs12543425	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530842	chr8:2292235-3249187	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv868862	chr8:2292235-3250958	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1015411	chr8:2301535-3153365	Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1017600	chr8:2498609-3168094	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv539339	chr8:2498609-3168094	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv915936	chr8:2498609-3179487	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv465340	chr8:2498609-3248652	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv609696	chr8:2498609-3248652	Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1033589	chr8:2498609-3305100	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1016899	chr8:2682086-3235154	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv539347	chr8:2682086-3235154	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1018407	chr8:2724294-3305100	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv915568	chr8:2725834-3291312	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1025408	chr8:2733604-3302447	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv889887	chr8:2740502-3143310	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1019842	chr8:2769114-3200810	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv539348	chr8:2769114-3200810	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1025622	chr8:3015881-3159246	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv539349	chr8:3015881-3159246	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1025209	chr8:3067655-3754882	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv1026643	chr8:3077210-3277827	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1026998	chr8:3102679-3593264	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv533642	chr8:3104559-3250929	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1031025	chr8:3119773-3209905	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv539350	chr8:3119773-3209905	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv609723	chr8:3134476-3143310	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:3141400-3142200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr8:3141600-3142200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr8:3141600-3142200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr8:3141600-3142200	Flanking Active TSS	Fetal Kidney	kidney
5	chr8:3141800-3142200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr8:3141800-3142200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:3141800-3142200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr8:3141800-3142200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr8:3141800-3142200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:3141800-3142200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr8:3141800-3142200	Enhancers	Adipose Nuclei	Adipose
12	chr8:3141800-3142200	Active TSS	Brain Angular Gyrus	brain
13	chr8:3141800-3142200	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr8:3141800-3142200	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr8:3141800-3142200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr8:3141800-3142200	Flanking Active TSS	Fetal Brain Male	brain
17	chr8:3141800-3142200	Flanking Active TSS	Fetal Brain Female	brain
18	chr8:3141800-3142200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
19	chr8:3141800-3142200	Flanking Active TSS	Fetal Lung	lung
20	chr8:3141800-3142200	Enhancers	Fetal Muscle Leg	muscle
21	chr8:3141800-3142200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr8:3142000-3142200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr8:3142000-3142200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr8:3142000-3142200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr8:3142000-3142200	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr8:3142000-3142200	Enhancers	Brain Germinal Matrix	brain
27	chr8:3142000-3142200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr8:3142000-3142200	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr8:3142000-3142200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr8:3142000-3142200	Active TSS	Fetal Muscle Trunk	muscle
31	chr8:3142000-3142200	Active TSS	Fetal Stomach	stomach

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