Variant report

Variant	rs62023768
Chromosome Location	chr15:99792471-99792472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:99790318-99793089	GM12891	blood:	n/a	n/a
2	BRCA1	chr15:99792106-99792525	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr15:99791037-99792538	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:99789370-99792567	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr15:99791797-99792492	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:99790665-99792519	PBDE	blood:	n/a	n/a
7	HCFC1	chr15:99788182-99792843	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:99643812..99646594-chr15:99789555..99792592,4	MCF-7	breast:
2	chr15:99788127..99791108-chr15:99792243..99793962,2	K562	blood:
3	chr15:99788657..99793033-chr15:100273651..100276844,5	MCF-7	breast:
4	chr15:99788127..99790475-chr15:99792462..99794073,2	K562	blood:
5	chr15:99790531..99793156-chr15:100244093..100247016,2	MCF-7	breast:

No data

Variant related genes	Relation type
TTC23	TF binding region
ENSG00000182253	Chromatin interaction
ENSG00000183060	Chromatin interaction
ENSG00000103852	Chromatin interaction
ENSG00000259475	Chromatin interaction
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1011041	0.97[ASN][1000 genomes]
rs28483588	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35892074	0.94[ASN][1000 genomes]
rs3743238	0.91[ASN][1000 genomes]
rs56854120	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60745649	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61141351	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023777	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023778	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023779	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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 miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
10	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62023768	LRRC28	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99788200-99792600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:99788400-99792600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:99788400-99792600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:99788400-99792600	Active TSS	Fetal Intestine Large	intestine
5	chr15:99788400-99792600	Active TSS	Right Ventricle	heart
6	chr15:99788400-99792800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr15:99788400-99792800	Active TSS	HSMMtube	muscle
8	chr15:99788600-99792600	Active TSS	Fetal Muscle Trunk	muscle
9	chr15:99788600-99792800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr15:99788800-99792800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:99788800-99792800	Active TSS	Fetal Stomach	stomach
12	chr15:99789000-99792600	Active TSS	Psoas Muscle	Psoas
13	chr15:99789400-99792600	Active TSS	Stomach Mucosa	stomach
14	chr15:99789400-99792600	Active TSS	Thymus	Thymus
15	chr15:99789600-99792800	Active TSS	Brain Germinal Matrix	brain
16	chr15:99789600-99792800	Active TSS	K562	blood
17	chr15:99790800-99792600	Active TSS	Left Ventricle	heart
18	chr15:99791000-99792600	Active TSS	Pancreas	Pancrea
19	chr15:99791800-99792800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr15:99791800-99792800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr15:99792000-99792600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr15:99792000-99792600	Weak transcription	Spleen	Spleen
23	chr15:99792000-99792800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:99792000-99792800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr15:99792000-99792800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr15:99792000-99792800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr15:99792000-99792800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:99792000-99792800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr15:99792000-99793000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr15:99792000-99793000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:99792000-99793000	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr15:99792000-99793000	Active TSS	Right Atrium	heart
33	chr15:99792200-99792600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:99792200-99792600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:99792200-99792600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
36	chr15:99792200-99792600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr15:99792200-99792600	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr15:99792200-99792600	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr15:99792200-99792600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr15:99792200-99792600	Flanking Active TSS	Fetal Heart	heart
41	chr15:99792200-99792600	Flanking Active TSS	HUVEC	blood vessel
42	chr15:99792200-99792600	Flanking Active TSS	Osteobl	bone
43	chr15:99792200-99792800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:99792200-99792800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:99792200-99792800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:99792200-99792800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:99792200-99792800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr15:99792200-99792800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr15:99792200-99792800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr15:99792200-99792800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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