Variant report

Variant	rs4965224
Chromosome Location	chr15:99788466-99788467
allele	C/G
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	SPI1	chr15:99788268-99789153	GM12878	blood:	n/a	chr15:99788693-99788706
2	FOXA2	chr15:99788229-99788553	HepG2	liver:	n/a	n/a
3	FOXA1	chr15:99788239-99788544	HepG2	liver:	n/a	n/a
4	MAFK	chr15:99788307-99788572	HepG2	liver:	n/a	n/a
5	FOXA1	chr15:99788246-99788666	HepG2	liver:	n/a	n/a
6	FOXA1	chr15:99788223-99788674	HepG2	liver:	n/a	n/a
7	FOXA1	chr15:99788242-99788626	HepG2	liver:	n/a	n/a
8	MAFK	chr15:99788397-99788621	HepG2	liver:	n/a	n/a
9	HCFC1	chr15:99788182-99792843	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99776229..99778768-chr15:99786778..99789073,2	K562	blood:

Variant related genes	Relation type
LRRC28	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10152912	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1223950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1223951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1238348	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12437806	0.99[ASN][1000 genomes]
rs12907394	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911768	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912927	0.91[YRI][hapmap]
rs12915819	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1567416	1.00[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976589	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976590	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048301	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2602030	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602036	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs2862139	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3937681	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4344722	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4965217	0.86[ASW][hapmap]
rs6598231	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164003	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7183226	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs7498053	0.83[YRI][hapmap]
rs8042021	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920418	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4965224	NR2F2	cis	cerebellum	SCAN
rs4965224	TTC23	cis	cerebellum	SCAN
rs4965224	SYNM	cis	parietal	SCAN
rs4965224	ADAMTS17	cis	parietal	SCAN
rs4965224	TTC23	cis	parietal	SCAN
rs4965224	NR2F2	cis	parietal	SCAN
rs4965224	SYNM	cis	cerebellum	SCAN
rs4965224	TTC23	cis	lymphoblastoid	seeQTL
rs4965224	TTC23	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99749800-99789400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:99750000-99789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:99756600-99789400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:99758600-99789400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:99759400-99788600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:99759400-99788600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:99762600-99789400	Weak transcription	Gastric	stomach
9	chr15:99765600-99789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:99765800-99789400	Weak transcription	Lung	lung
11	chr15:99768200-99788600	Weak transcription	Colonic Mucosa	Colon
12	chr15:99768200-99789200	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:99768800-99789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:99776600-99788800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:99782000-99789200	Weak transcription	Placenta	Placenta
16	chr15:99782200-99788600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:99782200-99788600	Weak transcription	Left Ventricle	heart
18	chr15:99782200-99789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:99782200-99789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:99782200-99789400	Weak transcription	Esophagus	oesophagus
21	chr15:99782200-99789400	Weak transcription	Pancreas	Pancrea
22	chr15:99782200-99791000	Weak transcription	Spleen	Spleen
23	chr15:99782400-99788600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:99787200-99788600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:99787200-99788600	Enhancers	Fetal Lung	lung
26	chr15:99787200-99788600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:99787400-99792400	Active TSS	GM12878-XiMat	blood
28	chr15:99787800-99788600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:99788000-99788600	Enhancers	Brain Germinal Matrix	brain
30	chr15:99788000-99788600	Enhancers	Rectal Smooth Muscle	rectum
31	chr15:99788000-99789000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr15:99788200-99788600	Enhancers	Adipose Nuclei	Adipose
33	chr15:99788200-99788600	Enhancers	Liver	Liver
34	chr15:99788200-99788600	Enhancers	Fetal Muscle Leg	muscle
35	chr15:99788200-99788800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:99788200-99788800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:99788200-99788800	Flanking Active TSS	NHEK	skin
38	chr15:99788200-99789000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:99788200-99789000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:99788200-99789000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr15:99788200-99789000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:99788200-99789000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:99788200-99789000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr15:99788200-99789000	Flanking Active TSS	A549	lung
45	chr15:99788200-99789000	Flanking Active TSS	Hela-S3	cervix
46	chr15:99788200-99789000	Flanking Active TSS	Osteobl	bone
47	chr15:99788200-99789200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:99788200-99789200	Enhancers	Stomach Mucosa	stomach
49	chr15:99788200-99789400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:99788200-99789400	Flanking Active TSS	Dnd41	blood

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