Variant report

Variant	rs9394996
Chromosome Location	chr6:44225723-44225724
allele	A/C
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	STAT3	chr6:44225436-44226631	GM12878	blood:	n/a	n/a
2	NR2F2	chr6:44225185-44226348	K562	blood:	n/a	chr6:44225487-44225502
3	MAX	chr6:44224555-44225759	K562	blood:	n/a	chr6:44225083-44225092 chr6:44224711-44224721 chr6:44225081-44225094 chr6:44225104-44225113 chr6:44225083-44225092 chr6:44225082-44225093 chr6:44225078-44225097 chr6:44225102-44225115
4	POU2F2	chr6:44224143-44226722	GM12878	blood:	n/a	chr6:44224710-44224722 chr6:44224715-44224727
5	YY1	chr6:44224781-44225849	GM12878	blood:	n/a	chr6:44225397-44225408 chr6:44224941-44224952 chr6:44225510-44225518 chr6:44224949-44224958
6	PML	chr6:44220368-44226860	GM12878	blood:	n/a	chr6:44223502-44223510
7	POLR2A	chr6:44214162-44225788	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:44214205-44227205	GM12891	blood:	n/a	n/a
9	EGR1	chr6:44225550-44225799	GM12878	blood:	n/a	chr6:44225674-44225688
10	SPI1	chr6:44225429-44225954	GM12891	blood:	n/a	n/a
11	CREB1	chr6:44224079-44225947	HepG2	liver:	n/a	n/a
12	IRF4	chr6:44225331-44225977	GM12878	blood:	n/a	n/a
13	MAX	chr6:44224218-44225841	ECC-1	luminal epithelium:	n/a	chr6:44225083-44225092 chr6:44224711-44224721 chr6:44225081-44225094 chr6:44225104-44225113 chr6:44225083-44225092 chr6:44225082-44225093 chr6:44225078-44225097 chr6:44225102-44225115
14	TBP	chr6:44224691-44225793	K562	blood:	n/a	n/a
15	RUNX3	chr6:44223554-44226547	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:44218235-44226207	Hela-S3	cervix:	n/a	n/a
17	CREB1	chr6:44224638-44225775	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:44220531-44227269	GM19099	blood:	n/a	n/a
19	CTCF	chr6:44225640-44225790	Caco-2	colon:	n/a	n/a
20	POLR2A	chr6:44224436-44225932	K562	blood:	n/a	n/a
21	POLR2A	chr6:44225357-44225882	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:44224621-44226417	HL-60	blood:	n/a	n/a
23	YY1	chr6:44224903-44225823	GM12878	blood:	n/a	chr6:44225397-44225408 chr6:44224941-44224952 chr6:44225510-44225518 chr6:44224949-44224958
24	POLR2A	chr6:44213452-44233528	GM12892	blood:	n/a	n/a
25	POLR2A	chr6:44220381-44226065	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr6:44213372-44233644	GM12891	blood:	n/a	n/a
27	NRF1	chr6:44225496-44226082	GM12878	blood:	n/a	n/a
28	POU2F2	chr6:44224581-44226530	GM12891	blood:	n/a	chr6:44224710-44224722 chr6:44224715-44224727
29	ZNF263	chr6:44224471-44226290	K562	blood:	n/a	chr6:44224805-44224814 chr6:44224704-44224713
30	CTCF	chr6:44225620-44225770	HCPEpiC	choroid plexus:	n/a	n/a
31	JUN	chr6:44221871-44226237	K562	blood:	n/a	n/a
32	POLR2A	chr6:44213396-44226181	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:44213416-44233519	GM12878	blood:	n/a	n/a
34	ELF1	chr6:44224531-44225936	GM12878	blood:	n/a	chr6:44224712-44224724
35	SP1	chr6:44225211-44225899	GM12878	blood:	n/a	n/a
36	MAX	chr6:44224270-44225906	HepG2	liver:	n/a	chr6:44225083-44225092 chr6:44224711-44224721 chr6:44225081-44225094 chr6:44225104-44225113 chr6:44225083-44225092 chr6:44225082-44225093 chr6:44225078-44225097 chr6:44225102-44225115
37	CHD1	chr6:44224547-44226862	GM12878	blood:	n/a	chr6:44225411-44225421 chr6:44224708-44224718
38	POLR2A	chr6:44212831-44226077	HepG2	liver:	n/a	n/a
39	GABPA	chr6:44224553-44225732	SK-N-SH	brain:	n/a	chr6:44225410-44225419 chr6:44224778-44224792 chr6:44224710-44224719
40	SPI1	chr6:44225531-44225829	GM12878	blood:	n/a	n/a
41	USF2	chr6:44224707-44226866	GM12878	blood:	n/a	chr6:44225105-44225114 chr6:44224713-44224729 chr6:44225098-44225119 chr6:44225104-44225113 chr6:44225102-44225115 chr6:44225104-44225113 chr6:44225103-44225112 chr6:44225081-44225092 chr6:44225102-44225113
42	POLR2A	chr6:44213292-44226484	K562	blood:	n/a	n/a
43	NFATC1	chr6:44224382-44226695	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:44213785-44233471	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:44224362-44227275	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:44213479-44233557	GM12892	blood:	n/a	n/a
47	EP300	chr6:44225321-44226571	GM12878	blood:	n/a	chr6:44225401-44225417
48	MEF2A	chr6:44224592-44225919	GM12878	blood:	n/a	n/a
49	NFATC1	chr6:44224383-44226557	GM12878	blood:	n/a	n/a
50	MAFK	chr6:44225026-44226246	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44223709..44226790-chr6:44264741..44266558,3	MCF-7	breast:
2	chr6:44107297..44110338-chr6:44222390..44225778,3	K562	blood:
3	chr6:44224914..44225770-chr6:44280677..44281261,3	MCF-7	breast:
4	chr6:44223567..44227779-chr6:44264321..44266816,4	MCF-7	breast:
5	chr6:44093370..44096253-chr6:44223564..44226835,7	K562	blood:
6	chr6:44225090..44228269-chr6:44308012..44310883,3	K562	blood:
7	chr10:102759072..102759859-chr6:44224918..44225866,2	HCT-116	colon:
8	chr6:44223815..44226053-chr6:44279566..44282424,2	MCF-7	breast:
9	chr6:44225012..44225889-chr6:44280928..44281605,2	K562	blood:
10	chr6:44102136..44105373-chr6:44223417..44225862,3	K562	blood:
11	chr6:44099546..44105774-chr6:44219938..44225862,7	K562	blood:
12	chr6:44094061..44096796-chr6:44223845..44226294,3	K562	blood:
13	chr6:44222000..44226440-chr6:44278583..44281839,6	K562	blood:

Variant related genes	Relation type
MIR4647	TF binding region
SLC35B2	TF binding region
ENSG00000146221	Chromatin interaction
ENSG00000107816	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000180992	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000249481	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11571891	1.00[AFR][1000 genomes]
rs12664825	1.00[ASW][hapmap]
rs3187	1.00[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs3734703	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778504	1.00[TSI][hapmap]
rs760370	0.83[JPT][hapmap]
rs9367190	1.00[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs9381303	1.00[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885855	chr6:44223010-44231479	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
12	nsv885856	chr6:44223010-44232920	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
13	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9394996	SLC29A1	cis	lymphoblastoid	seeQTL
rs9394996	ENSG00000157593	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44223600-44226000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:44223800-44225800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:44223800-44226000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:44224000-44225800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:44224000-44225800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:44224000-44225800	Active TSS	A549	lung
7	chr6:44224200-44225800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:44224200-44225800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:44224200-44225800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:44224200-44226000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:44224200-44226000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr6:44224600-44226000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:44224800-44225800	Active TSS	Left Ventricle	heart
14	chr6:44224800-44226400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:44225400-44225800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:44225400-44225800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:44225400-44225800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:44225400-44225800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:44225400-44225800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:44225400-44225800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:44225400-44225800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:44225400-44225800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr6:44225400-44225800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr6:44225400-44225800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:44225400-44225800	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr6:44225400-44225800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr6:44225400-44225800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:44225400-44225800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr6:44225400-44225800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr6:44225400-44225800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr6:44225400-44225800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr6:44225400-44225800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:44225400-44225800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr6:44225400-44225800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:44225400-44225800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr6:44225400-44225800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:44225400-44225800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:44225400-44225800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:44225400-44225800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:44225400-44225800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr6:44225400-44225800	Flanking Active TSS	Liver	Liver
42	chr6:44225400-44225800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:44225400-44225800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr6:44225400-44225800	Flanking Active TSS	Fetal Brain Female	brain
45	chr6:44225400-44225800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr6:44225400-44225800	Flanking Active TSS	Fetal Lung	lung
47	chr6:44225400-44225800	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr6:44225400-44225800	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr6:44225400-44225800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:44225400-44225800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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