Variant report

Variant	rs2280786
Chromosome Location	chr17:34257637-34257638
allele	A/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	YY1	chr17:34257428-34257950	GM12892	blood:	n/a	n/a
2	YY1	chr17:34257530-34257951	GM12878	blood:	n/a	n/a
3	E2F6	chr17:34257466-34257938	K562	blood:	n/a	chr17:34257776-34257785
4	GTF2F1	chr17:34257550-34258011	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:34257545-34258139	K562	blood:	n/a	n/a
6	TBP	chr17:34257595-34258132	K562	blood:	n/a	n/a
7	E2F6	chr17:34257561-34258081	A549	lung:	n/a	chr17:34257776-34257785
8	NRF1	chr17:34257569-34258041	GM12878	blood:	n/a	chr17:34257775-34257786 chr17:34257777-34257786 chr17:34257743-34257754 chr17:34257814-34257823 chr17:34257772-34257786 chr17:34257775-34257789 chr17:34257775-34257786
9	SP1	chr17:34257604-34257917	GM12878	blood:	n/a	chr17:34257823-34257835 chr17:34257824-34257833 chr17:34257825-34257834 chr17:34257825-34257834
10	POLR2A	chr17:34257458-34257959	MCF-7	breast:	n/a	n/a
11	POLR2A	chr17:34257518-34257850	GM12878	blood:	n/a	n/a
12	E2F4	chr17:34257473-34258524	MCF10A-Er-Src	breast:	n/a	chr17:34257776-34257785
13	YY1	chr17:34257505-34257906	ECC-1	luminal epithelium:	n/a	n/a
14	YY1	chr17:34257583-34258027	K562	blood:	n/a	n/a
15	IRF1	chr17:34257584-34258162	K562	blood:	n/a	chr17:34257823-34257837
16	CHD2	chr17:34257548-34258043	GM12878	blood:	n/a	n/a
17	E2F6	chr17:34257514-34258039	H1-hESC	embryonic stem cell:	n/a	chr17:34257776-34257785
18	E2F4	chr17:34257595-34258016	GM12878	blood:	n/a	chr17:34257776-34257785
19	E2F6	chr17:34257064-34258140	H1-hESC	embryonic stem cell:	n/a	chr17:34257776-34257785
20	E2F4	chr17:34257561-34258005	K562	blood:	n/a	chr17:34257776-34257785
21	POLR2A	chr17:34257349-34258087	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F4	chr17:34257565-34257987	Hela-S3	cervix:	n/a	chr17:34257776-34257785
23	POLR2A	chr17:34257348-34258295	U87	brain:	n/a	n/a
24	E2F6	chr17:34257251-34258015	K562	blood:	n/a	chr17:34257776-34257785
25	ATF3	chr17:34257587-34258081	A549	lung:	n/a	n/a
26	POLR2A	chr17:34257481-34258179	H1-hESC	embryonic stem cell:	n/a	n/a
27	SETDB1	chr17:34257550-34258191	U2OS	brain:	n/a	chr17:34257776-34257785
28	IRF1	chr17:34257491-34258130	K562	blood:	n/a	chr17:34257823-34257837
29	POLR2A	chr17:34257394-34258112	GM12892	blood:	n/a	n/a
30	POLR2A	chr17:34257525-34257798	A549	lung:	n/a	n/a
31	ATF3	chr17:34257493-34258046	A549	lung:	n/a	n/a
32	UBTF	chr17:34257368-34258164	K562	blood:	n/a	n/a
33	BHLHE40	chr17:34257613-34258093	K562	blood:	n/a	n/a
34	POLR2A	chr17:34257568-34257879	GM12891	blood:	n/a	n/a
35	POLR2A	chr17:34257432-34258140	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr17:34257549-34257803	GM12892	blood:	n/a	n/a
37	MAX	chr17:34257567-34258048	K562	blood:	n/a	n/a
38	MAX	chr17:34257589-34258100	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr17:34257323-34258121	GM12891	blood:	n/a	n/a
40	MXI1	chr17:34257425-34258136	GM12878	blood:	n/a	n/a
41	POLR2A	chr17:34257580-34257838	H1-hESC	embryonic stem cell:	n/a	n/a
42	PAX5	chr17:34257541-34258049	GM12878	blood:	n/a	n/a
43	POLR2A	chr17:34257524-34258063	GM18951	blood:	n/a	n/a
44	REST	chr17:34257163-34257967	A549	lung:	n/a	n/a
45	POLR2A	chr17:34257496-34258058	K562	blood:	n/a	n/a
46	TAF1	chr17:34257559-34258080	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr17:34257212-34259498	K562	blood:	n/a	n/a
48	POLR2A	chr17:34257573-34258040	H1-hESC	embryonic stem cell:	n/a	n/a
49	TBL1XR1	chr17:34257552-34258291	K562	blood:	n/a	n/a
50	POLR2A	chr17:34257540-34258143	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RDM1-2	chr17:34257636-34257780	NR_027996

Variant related genes	Relation type
RDM1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10451309	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2072667	0.83[AMR][1000 genomes]
rs2242596	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280783	1.00[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2280788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2526331	0.89[EUR][1000 genomes]
rs2702958	0.89[EUR][1000 genomes]
rs2735499	0.89[EUR][1000 genomes]
rs28914802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28914816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28914817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28914819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4251700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4251704	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4251710	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4251739	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55680144	0.89[EUR][1000 genomes]
rs55781042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55792948	0.89[EUR][1000 genomes]
rs55799023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55833673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55846484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55906604	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55915639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55951822	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56029903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56077005	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56111312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56135703	1.00[AFR][1000 genomes]
rs56170514	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56181735	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56221144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56262662	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56305516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56347933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56382694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61737011	0.83[AMR][1000 genomes]
rs62078115	0.83[AMR][1000 genomes]
rs72483217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	esv3380735	chr17:34246253-34271932	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1063100	chr17:34246253-34397598	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833424	chr17:34246253-34419476	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1056950	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1059795	chr17:34246253-34442620	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060457	chr17:34246253-34442620	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv543320	chr17:34246253-34442620	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv949160	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2280786	CCL3L1	cis	lymphoblastoid	seeQTL
rs2280786	CCL3	cis	lymphoblastoid	seeQTL
rs2280786	RDM1	cis	lymphoblastoid	seeQTL
rs2280786	CCL5	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34256800-34258000	Flanking Active TSS	Fetal Thymus	thymus
2	chr17:34257000-34257800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr17:34257000-34257800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:34257000-34257800	Enhancers	Lung	lung
5	chr17:34257000-34258000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:34257000-34258000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr17:34257000-34258000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:34257000-34258000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:34257000-34258000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr17:34257000-34258000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr17:34257000-34258000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr17:34257000-34258000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:34257000-34258000	Enhancers	Colon Smooth Muscle	Colon
14	chr17:34257000-34258000	Active TSS	Fetal Intestine Large	intestine
15	chr17:34257000-34258000	Active TSS	Fetal Kidney	kidney
16	chr17:34257000-34258000	Flanking Active TSS	Fetal Stomach	stomach
17	chr17:34257000-34258000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr17:34257000-34258000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr17:34257000-34258000	Active TSS	Rectal Smooth Muscle	rectum
20	chr17:34257000-34258000	Flanking Active TSS	HMEC	breast
21	chr17:34257000-34258200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:34257000-34258200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr17:34257000-34258200	Flanking Active TSS	Osteobl	bone
27	chr17:34257200-34257800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr17:34257200-34257800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr17:34257200-34257800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr17:34257200-34257800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:34257200-34257800	Enhancers	Spleen	Spleen
32	chr17:34257200-34257800	Active TSS	GM12878-XiMat	blood
33	chr17:34257200-34257800	Active TSS	K562	blood
34	chr17:34257200-34257800	Active TSS	NHLF	lung
35	chr17:34257200-34258000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:34257200-34258000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:34257200-34258000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr17:34257200-34258000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr17:34257200-34258000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr17:34257200-34258000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:34257200-34258000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr17:34257200-34258000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:34257200-34258000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
44	chr17:34257200-34258000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr17:34257200-34258000	Flanking Active TSS	Fetal Brain Male	brain
46	chr17:34257200-34258000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr17:34257200-34258000	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr17:34257200-34258000	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr17:34257200-34258000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr17:34257200-34258000	Flanking Active TSS	Thymus	Thymus

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