Variant report

Variant	rs13067629
Chromosome Location	chr3:121378287-121378288
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	POLR2A	chr3:121377940-121378365	GM12892	blood:	n/a	n/a
2	WRNIP1	chr3:121378160-121380048	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:121378045-121380888	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:121376697-121380815	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:121377924-121380942	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:121377943-121380122	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:121378109-121380470	GM18505	blood:	n/a	n/a
8	POLR2A	chr3:121377978-121380138	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:121377905-121380414	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:121377985-121378736	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121377179..121379153-chr3:121573085..121574882,2	MCF-7	breast:

Variant related genes	Relation type
RNU4-62P	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12489511	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12490565	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs12631824	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1492177	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1574655	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1574735	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1873645	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1919552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1919557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1986351	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1986874	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001390	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2070179	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2840143	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35295338	0.89[EUR][1000 genomes]
rs3772127	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4478028	0.85[EUR][1000 genomes]
rs4676684	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4676685	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4676686	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438645	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438660	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6791896	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794341	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6794677	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6802033	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7375038	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7429247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7430165	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611913	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7620842	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7646346	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs7646585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289172	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289173	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9681209	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs9809114	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9829053	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9832267	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835182	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854052	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861992	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876021	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13067629	HCLS1	cis	Lymphoblastoid	GTEx
rs13067629	HCLS1	cis	multi-tissue	Pritchard
rs13067629	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
2	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
3	chr3:121351400-121381400	Weak transcription	Gastric	stomach
4	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:121362200-121379400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:121362600-121379600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:121364200-121378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:121367400-121379000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:121367400-121381800	Weak transcription	Pancreas	Pancrea
11	chr3:121367600-121378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:121367800-121378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:121368800-121380000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:121370600-121379400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:121370600-121381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
17	chr3:121372600-121379000	Weak transcription	Fetal Heart	heart
18	chr3:121373000-121380400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:121374000-121379600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:121374800-121380000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:121376200-121378400	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr3:121376200-121378400	Weak transcription	Placenta	Placenta
23	chr3:121376400-121382200	Weak transcription	A549	lung
24	chr3:121376400-121383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:121376800-121378400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr3:121376800-121378600	Genic enhancers	Fetal Thymus	thymus
27	chr3:121376800-121378800	Enhancers	Right Atrium	heart
28	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:121377200-121379200	Weak transcription	Esophagus	oesophagus
30	chr3:121377400-121378400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:121377400-121379400	Enhancers	Lung	lung
32	chr3:121377400-121380800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr3:121377600-121378800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:121377600-121379200	Enhancers	Left Ventricle	heart
35	chr3:121377600-121379200	Enhancers	Spleen	Spleen
36	chr3:121377600-121379400	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr3:121377600-121379600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:121377800-121378600	Enhancers	HUVEC	blood vessel
39	chr3:121377800-121379400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:121377800-121379400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr3:121377800-121381600	Weak transcription	Fetal Brain Female	brain
42	chr3:121378000-121378400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:121378000-121378400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
44	chr3:121378000-121378400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr3:121378000-121378400	Active TSS	Brain Substantia Nigra	brain
46	chr3:121378000-121378600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
47	chr3:121378000-121378600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr3:121378000-121378600	Genic enhancers	Thymus	Thymus
49	chr3:121378000-121379000	Enhancers	Fetal Muscle Leg	muscle
50	chr3:121378000-121379000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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