Variant report

Variant	rs28646033
Chromosome Location	chr3:85008511-85008512
allele	G/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	CTCF	chr3:85008400-85008550	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr3:85008450-85008576	MCF-7	breast:	n/a	n/a
3	CTCF	chr3:85008420-85008570	HA-sp	spinal cord:	n/a	n/a
4	CTCF	chr3:85008420-85008570	HPAF	blood vessel:	n/a	n/a
5	JUND	chr3:85008348-85008539	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:85008400-85008550	HRPEpiC	eye:	n/a	n/a
7	MAX	chr3:85007487-85008599	ECC-1	luminal epithelium:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
8	MAX	chr3:85007409-85008751	A549	lung:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
9	TAF1	chr3:85007638-85008549	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:85007453-85008645	ECC-1	luminal epithelium:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
11	SP1	chr3:85007498-85009254	H1-hESC	embryonic stem cell:	n/a	chr3:85008037-85008047 chr3:85008091-85008101 chr3:85008933-85008945 chr3:85007803-85007813 chr3:85008934-85008948 chr3:85008090-85008102 chr3:85008933-85008945 chr3:85008036-85008048 chr3:85007803-85007813 chr3:85008823-85008835 chr3:85008935-85008944 chr3:85008824-85008833 chr3:85008090-85008102 chr3:85008038-85008047 chr3:85007624-85007634 chr3:85008824-85008833 chr3:85008092-85008101 chr3:85007803-85007817 chr3:85007803-85007812 chr3:85007812-85007833 chr3:85008092-85008101 chr3:85007802-85007814 chr3:85008091-85008100 chr3:85008064-85008073 chr3:85008062-85008074 chr3:85008037-85008046 chr3:85008087-85008101 chr3:85007802-85007814 chr3:85008825-85008834 chr3:85008091-85008101 chr3:85007804-85007813 chr3:85008010-85008031 chr3:85007803-85007812 chr3:85007953-85007966
12	POLR2A	chr3:85007683-85009152	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:85008437-85008562	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:85007333-85008819	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr3:85007591-85008616	MCF-7	breast:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
16	MXI1	chr3:85007415-85011781	SK-N-SH	brain:	n/a	n/a
17	E2F6	chr3:85007456-85008625	A549	lung:	n/a	chr3:85007804-85007813 chr3:85008091-85008100 chr3:85007823-85007832
18	EP300	chr3:85007861-85008518	ECC-1	luminal epithelium:	n/a	n/a
19	MYC	chr3:85008112-85008700	MCF-7	breast:	n/a	n/a
20	MXI1	chr3:85008226-85008547	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD1	chr3:85008169-85008877	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:85007722-85009541	H1-neurons	neurons:	n/a	n/a
23	CTCF	chr3:85008420-85008570	HAc	cerebellar:	n/a	n/a
24	POLR2A	chr3:85007681-85008676	H1-neurons	neurons:	n/a	n/a
25	CHD2	chr3:85007616-85008518	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3A	chr3:85007498-85011149	H1-hESC	embryonic stem cell:	n/a	chr3:85008956-85008967 chr3:85007753-85007766
27	TAF1	chr3:85007505-85009261	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr3:85008380-85008530	HMEC	breast:	n/a	n/a
29	E2F6	chr3:85007596-85008710	H1-hESC	embryonic stem cell:	n/a	chr3:85007804-85007813 chr3:85008091-85008100 chr3:85007823-85007832
30	MAX	chr3:85007564-85008606	HepG2	liver:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
31	MAX	chr3:85007557-85008672	SK-N-SH	brain:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
32	MAX	chr3:85007536-85008608	A549	lung:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
33	CTCF	chr3:85008460-85008610	HCM	heart:	n/a	n/a
34	CTCF	chr3:85008420-85008570	AG04449	skin:	n/a	n/a
35	CTCF	chr3:85008380-85008530	SK-N-SH_RA	brain:	n/a	n/a
36	JUND	chr3:85008231-85009202	H1-hESC	embryonic stem cell:	n/a	chr3:85009024-85009035
37	MAX	chr3:85007524-85008643	HepG2	liver:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
38	MAX	chr3:85007559-85008697	H1-hESC	embryonic stem cell:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
39	MXI1	chr3:85007589-85008588	HepG2	liver:	n/a	n/a
40	E2F6	chr3:85008008-85008642	H1-hESC	embryonic stem cell:	n/a	chr3:85008091-85008100
41	CTCF	chr3:85008500-85008650	HEEpiC	esophagus:	n/a	n/a
42	CTBP2	chr3:85008265-85009372	H1-hESC	embryonic stem cell:	n/a	n/a
43	REST	chr3:85007703-85009644	H1-neurons	neurons:	n/a	chr3:85007753-85007766 chr3:85007921-85007935
44	MAX	chr3:85007516-85008705	HepG2	liver:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
45	ZNF143	chr3:85007545-85008981	H1-hESC	embryonic stem cell:	n/a	chr3:85008831-85008841
46	RAD21	chr3:85007565-85009382	H1-hESC	embryonic stem cell:	n/a	chr3:85008060-85008072 chr3:85008959-85008971 chr3:85008959-85008969 chr3:85008032-85008041
47	POLR2A	chr3:85007660-85008660	MCF-7	breast:	n/a	n/a
48	CTCF	chr3:85008400-85008550	WERI-Rb-1	eye:	n/a	n/a
49	CTCF	chr3:85008138-85008580	MCF-7	breast:	n/a	n/a
50	TAF1	chr3:85007864-85008802	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP2B-6	chr3:85008156-85008819	NONHSAT090658
2	lnc-CHMP2B-6	chr3:85008140-85008643	NONHSAT090657

Variant related genes	Relation type
CADM2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17420038	1.00[AFR][1000 genomes]
rs17420520	1.00[AFR][1000 genomes]
rs17503522	1.00[AFR][1000 genomes]
rs17734184	1.00[AFR][1000 genomes]
rs17734437	1.00[AFR][1000 genomes]
rs17791224	1.00[AFR][1000 genomes]
rs1872555	1.00[AFR][1000 genomes]
rs2036062	1.00[AFR][1000 genomes]
rs6796144	1.00[AFR][1000 genomes]
rs73125134	1.00[AFR][1000 genomes]
rs73137632	1.00[AFR][1000 genomes]
rs73137640	1.00[AFR][1000 genomes]
rs73137663	1.00[AFR][1000 genomes]
rs73139661	1.00[AFR][1000 genomes]
rs73139674	1.00[AFR][1000 genomes]
rs73139689	1.00[AFR][1000 genomes]
rs73139694	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85007200-85008800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr3:85007200-85009600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:85007200-85011800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr3:85007200-85012400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:85007200-85012600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:85007400-85008600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:85007400-85008800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:85007400-85008800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:85007400-85008800	Active TSS	NH-A	brain
10	chr3:85007400-85009200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:85007400-85009200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:85007400-85009600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:85007400-85009800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr3:85007400-85009800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:85007400-85011200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:85007400-85011600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:85007400-85012000	Active TSS	Brain Cingulate Gyrus	brain
18	chr3:85007600-85008600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:85007600-85008600	Bivalent/Poised TSS	Fetal Kidney	kidney
20	chr3:85007600-85008600	Bivalent/Poised TSS	Thymus	Thymus
21	chr3:85007600-85008600	Active TSS	A549	lung
22	chr3:85007600-85008600	Active TSS	Hela-S3	cervix
23	chr3:85007600-85008600	Active TSS	HSMMtube	muscle
24	chr3:85007600-85008600	Active TSS	NHEK	skin
25	chr3:85007600-85008600	Active TSS	NHLF	lung
26	chr3:85007600-85008800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:85007600-85008800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr3:85007600-85008800	Flanking Active TSS	Ovary	ovary
29	chr3:85007600-85008800	Active TSS	Psoas Muscle	Psoas
30	chr3:85007600-85008800	Flanking Active TSS	Right Ventricle	heart
31	chr3:85007600-85008800	Active TSS	NHDF-Ad	bronchial
32	chr3:85007600-85009200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr3:85007600-85009200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:85007600-85009200	Active TSS	Aorta	Aorta
35	chr3:85007600-85009600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr3:85007600-85010000	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr3:85007600-85010000	ZNF genes & repeats	Spleen	Spleen
38	chr3:85007600-85010200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:85007600-85011000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:85007600-85011200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:85007600-85012200	Active TSS	Brain Anterior Caudate	brain
42	chr3:85007800-85008600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:85007800-85008600	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:85007800-85008600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:85007800-85008600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:85007800-85008600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:85007800-85008600	Active TSS	Fetal Heart	heart
48	chr3:85007800-85008600	Bivalent/Poised TSS	Fetal Lung	lung
49	chr3:85007800-85008600	Bivalent/Poised TSS	Fetal Stomach	stomach
50	chr3:85007800-85008600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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