Variant report

Variant	rs7164003
Chromosome Location	chr15:99822302-99822303
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	ZNF384	chr15:99822260-99822626	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:99822262-99822380	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99820578..99822487-chr15:99824198..99826248,2	MCF-7	breast:

Variant related genes	Relation type
LRRC28	TF binding region
ENSG00000259228	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10152912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1223950	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1223951	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1238348	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12437806	0.95[ASN][1000 genomes]
rs12907394	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12911768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912927	1.00[YRI][hapmap]
rs12915819	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567416	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1976590	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2602030	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602036	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2862139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3937681	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4246296	0.82[ASN][1000 genomes]
rs4344722	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965217	0.86[ASW][hapmap]
rs4965224	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]
rs6598231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183226	0.82[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs7498053	1.00[YRI][hapmap]
rs8042021	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920418	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv977760	chr15:99817087-99826056	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7164003	TTC23	cis	parietal	SCAN
rs7164003	TTC23	cis	cerebellum	SCAN
rs7164003	NR2F2	cis	parietal	SCAN
rs7164003	SYNM	cis	cerebellum	SCAN
rs7164003	ADAMTS17	cis	parietal	SCAN
rs7164003	TTC23	cis	lymphoblastoid	seeQTL
rs7164003	TTC23	cis	multi-tissue	Pritchard
rs7164003	SYNM	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792200-99846400	Weak transcription	Lung	lung
2	chr15:99792600-99832200	Weak transcription	Aorta	Aorta
3	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
4	chr15:99793000-99823800	Weak transcription	Fetal Brain Male	brain
5	chr15:99793000-99838000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:99793000-99850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:99793000-99866600	Weak transcription	Gastric	stomach
8	chr15:99793200-99822400	Weak transcription	Adipose Nuclei	Adipose
9	chr15:99794000-99830800	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:99794000-99840000	Weak transcription	Brain Anterior Caudate	brain
11	chr15:99794000-99846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:99794200-99834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:99794200-99847000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:99794400-99845200	Weak transcription	HSMMtube	muscle
15	chr15:99798000-99838200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:99798400-99831200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:99798400-99834600	Weak transcription	HSMM	muscle
18	chr15:99799400-99838200	Weak transcription	Fetal Lung	lung
19	chr15:99799600-99824800	Weak transcription	Left Ventricle	heart
20	chr15:99800000-99834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:99803200-99832200	Weak transcription	Fetal Stomach	stomach
22	chr15:99808800-99845200	Weak transcription	Fetal Kidney	kidney
23	chr15:99809000-99828000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:99809000-99830800	Weak transcription	Fetal Intestine Large	intestine
25	chr15:99809000-99846400	Weak transcription	Pancreas	Pancrea
26	chr15:99809000-99846400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:99813800-99822600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:99814200-99838400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:99814400-99823800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:99814600-99824000	Weak transcription	Osteobl	bone
31	chr15:99816200-99824000	Weak transcription	Fetal Heart	heart
32	chr15:99816200-99828800	Weak transcription	Fetal Intestine Small	intestine
33	chr15:99816200-99832200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:99816400-99838800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:99816800-99846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:99817000-99845000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:99817200-99834000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:99817200-99834400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:99818800-99824200	Weak transcription	Fetal Brain Female	brain
40	chr15:99819000-99822400	Enhancers	Fetal Thymus	thymus
41	chr15:99819400-99834600	Weak transcription	Primary B cells from cord blood	blood
42	chr15:99819600-99822600	Flanking Active TSS	Dnd41	blood
43	chr15:99819600-99838200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:99819800-99854800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:99820000-99823200	Enhancers	Thymus	Thymus
46	chr15:99820000-99828000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:99820000-99831000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:99820000-99834600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:99820000-99836400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:99820000-99836400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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