Variant report

Variant	rs1864753
Chromosome Location	chr6:36812230-36812231
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	BHLHE40	chr6:36811983-36812356	K562	blood:	n/a	n/a
2	EGR1	chr6:36811924-36812232	K562	blood:	n/a	chr6:36812144-36812155 chr6:36812143-36812156 chr6:36812143-36812156
3	EGR1	chr6:36811982-36812267	K562	blood:	n/a	chr6:36812144-36812155 chr6:36812143-36812156 chr6:36812143-36812156
4	RCOR1	chr6:36812020-36812241	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36811002..36813494-chr6:36814165..36817730,3	MCF-7	breast:
2	chr6:36807425..36809491-chr6:36809760..36812415,2	MCF-7	breast:
3	chr6:36811312..36813099-chr6:36818892..36821190,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE5-1	chr6:36811983-36812383	XLOC_005701
2	lnc-CPNE5-1	chr6:36811983-36812352	NONHSAT112233

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10456445	0.84[EUR][1000 genomes]
rs11964396	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12111266	0.96[EUR][1000 genomes]
rs12111291	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12524018	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12524422	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12524649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12525180	0.82[EUR][1000 genomes]
rs12525540	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12526699	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12529199	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12529769	0.94[EUR][1000 genomes]
rs17374068	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17552561	0.82[EUR][1000 genomes]
rs35694858	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41408445	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4348312	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4714013	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55681762	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55913388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56240344	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56302344	0.96[EUR][1000 genomes]
rs66474948	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66566790	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67273613	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68042914	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72846046	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72846078	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73416282	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7745555	0.96[EUR][1000 genomes]
rs9470418	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats 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	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36808600-36818800	Weak transcription	Dnd41	blood
2	chr6:36808800-36816000	Weak transcription	Spleen	Spleen
3	chr6:36808800-36816600	Weak transcription	Aorta	Aorta
4	chr6:36809000-36813800	Enhancers	Fetal Muscle Leg	muscle
5	chr6:36809000-36816600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:36809000-36818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
8	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:36809200-36812400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:36809200-36812400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:36809200-36812600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:36809200-36812600	Weak transcription	Fetal Brain Female	brain
13	chr6:36809200-36816000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:36809200-36817000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:36809200-36818000	Weak transcription	HSMM	muscle
16	chr6:36809200-36819200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:36809400-36812400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:36809400-36812400	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:36809800-36818400	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:36810000-36813000	Enhancers	Fetal Muscle Trunk	muscle
21	chr6:36810800-36812400	Enhancers	Psoas Muscle	Psoas
22	chr6:36810800-36813800	Enhancers	Fetal Heart	heart
23	chr6:36811000-36815400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:36811000-36816000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:36811000-36816000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:36811200-36814000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:36811200-36815000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:36811400-36813200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
30	chr6:36811600-36816200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:36811800-36813800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:36812000-36813400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:36812000-36814400	Enhancers	K562	blood
34	chr6:36812200-36812400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr6:36812200-36812400	Weak transcription	Right Atrium	heart
36	chr6:36812200-36812600	Enhancers	Brain Germinal Matrix	brain
37	chr6:36812200-36812600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr6:36812200-36813000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr6:36812200-36813400	Enhancers	Left Ventricle	heart
40	chr6:36812200-36814000	Enhancers	Right Ventricle	heart

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