Variant report

Variant	rs730775
Chromosome Location	chr6:44232074-44232075
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	SPI1	chr6:44231895-44232429	HL-60	blood:	n/a	chr6:44232142-44232155 chr6:44232141-44232154 chr6:44232143-44232152 chr6:44232142-44232155 chr6:44232160-44232173
2	ELF1	chr6:44231883-44232407	K562	blood:	n/a	chr6:44232160-44232171 chr6:44232159-44232172 chr6:44232143-44232154
3	NFATC1	chr6:44230615-44232531	GM12878	blood:	n/a	n/a
4	UBTF	chr6:44231806-44232303	K562	blood:	n/a	n/a
5	BCLAF1	chr6:44229967-44232867	GM12878	blood:	n/a	chr6:44232448-44232457 chr6:44231117-44231126 chr6:44230517-44230526 chr6:44231116-44231125
6	MAFK	chr6:44231903-44232267	K562	blood:	n/a	chr6:44231984-44231999
7	MAX	chr6:44231969-44232294	K562	blood:	n/a	n/a
8	TAF1	chr6:44231909-44232316	GM12891	blood:	n/a	n/a
9	YY1	chr6:44230835-44232368	GM12878	blood:	n/a	n/a
10	RELA	chr6:44230400-44233646	GM18505	blood:	n/a	chr6:44230761-44230770 chr6:44230761-44230770 chr6:44231328-44231337 chr6:44231328-44231337
11	MAX	chr6:44231912-44233625	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:44213452-44233528	GM12892	blood:	n/a	n/a
13	ELF1	chr6:44231896-44232384	GM12878	blood:	n/a	chr6:44232160-44232171 chr6:44232159-44232172 chr6:44232143-44232154
14	POLR2A	chr6:44231146-44233514	Raji	blood:	n/a	n/a
15	POLR2A	chr6:44213372-44233644	GM12891	blood:	n/a	n/a
16	STAT5A	chr6:44229584-44233087	GM12878	blood:	n/a	chr6:44231139-44231150 chr6:44230531-44230543 chr6:44231312-44231320 chr6:44231460-44231468 chr6:44229749-44229761
17	MAX	chr6:44231886-44233615	GM12878	blood:	n/a	n/a
18	CTCF	chr6:44232000-44233374	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:44213416-44233519	GM12878	blood:	n/a	n/a
20	EP300	chr6:44231772-44232302	GM12878	blood:	n/a	chr6:44232064-44232077 chr6:44232139-44232153 chr6:44232162-44232171
21	POLR2A	chr6:44231988-44232299	HUVEC	blood vessel:	n/a	n/a
22	FOXM1	chr6:44231822-44232459	GM12878	blood:	n/a	chr6:44232031-44232039
23	CEBPB	chr6:44230373-44232307	GM12878	blood:	n/a	n/a
24	TAF1	chr6:44231981-44232285	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:44229240-44233577	GM18951	blood:	n/a	n/a
26	SPI1	chr6:44231977-44232257	GM12878	blood:	n/a	chr6:44232142-44232155 chr6:44232141-44232154 chr6:44232143-44232152 chr6:44232142-44232155 chr6:44232160-44232173
27	POLR2A	chr6:44229697-44233440	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:44213785-44233471	GM12878	blood:	n/a	n/a
29	TCF12	chr6:44231987-44232269	GM12878	blood:	n/a	n/a
30	WRNIP1	chr6:44229636-44233069	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:44213479-44233557	GM12892	blood:	n/a	n/a
32	STAT5A	chr6:44231305-44232462	GM12878	blood:	n/a	chr6:44231312-44231320 chr6:44231460-44231468
33	SPI1	chr6:44231820-44232402	GM12891	blood:	n/a	chr6:44232142-44232155 chr6:44232141-44232154 chr6:44232143-44232152 chr6:44232142-44232155 chr6:44232160-44232173
34	POLR2A	chr6:44229166-44233419	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:44231989-44233617	K562	blood:	n/a	n/a
36	RCOR1	chr6:44232057-44233600	Hela-S3	cervix:	n/a	n/a
37	MAZ	chr6:44231882-44232311	K562	blood:	n/a	n/a
38	POLR2A	chr6:44231289-44232247	K562	blood:	n/a	n/a
39	EBF1	chr6:44232035-44232736	GM12878	blood:	n/a	chr6:44232236-44232247
40	CCNT2	chr6:44232050-44232312	K562	blood:	n/a	n/a
41	EBF1	chr6:44232049-44232430	GM12878	blood:	n/a	chr6:44232236-44232247
42	CTCF	chr6:44232067-44232362	K562	blood:	n/a	n/a
43	MAX	chr6:44231888-44233559	NB4	blood:	n/a	n/a
44	MTA3	chr6:44229970-44232487	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:44229138-44233380	GM12891	blood:	n/a	n/a
46	POLR2A	chr6:44229960-44233576	GM15510	blood:	n/a	n/a
47	HCFC1	chr6:44232006-44232286	K562	blood:	n/a	n/a
48	SPI1	chr6:44231759-44232548	HL-60	blood:	n/a	chr6:44232142-44232155 chr6:44232141-44232154 chr6:44232143-44232152 chr6:44232142-44232155 chr6:44232160-44232173
49	ATF2	chr6:44230321-44232776	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:44229243-44233544	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44230152..44232181-chr6:44314660..44317132,2	K562	blood:
2	chr6:44231911..44234847-chr6:44237510..44240187,2	MCF-7	breast:
3	chr6:44093102..44095527-chr6:44231141..44233414,2	MCF-7	breast:
4	chr6:44092343..44095710-chr6:44231665..44234902,4	K562	blood:
5	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
6	chr6:44229471..44232092-chr6:44306709..44308642,2	K562	blood:
7	chr6:44231038..44232613-chr6:44324108..44326590,2	K562	blood:
8	chr6:44100637..44102842-chr6:44230503..44233422,2	MCF-7	breast:
9	chr6:43624198..43626185-chr6:44230029..44232355,2	K562	blood:
10	chr6:44231156..44234544-chr6:44279395..44281173,3	MCF-7	breast:
11	chr6:44231603..44235224-chr6:44277267..44282023,5	MCF-7	breast:
12	chr6:44231713..44233466-chr6:44264708..44267385,2	MCF-7	breast:

Variant related genes	Relation type
NFKBIE	TF binding region
ENSG00000146221	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000096401	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000178233	Chromatin interaction
ENSG00000180992	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1283567	0.89[ASN][1000 genomes]
rs2233437	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs324137	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs325001	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs3799962	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483536	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs498512	0.81[JPT][hapmap]
rs513688	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs639728	0.84[CEU][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs651297	0.86[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
12	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs730775	NT5DC2	trans	cerebellum	SCAN
rs730775	HSP90AB1	cis	cerebellum	SCAN
rs730775	TCTE1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44225600-44232600	Weak transcription	Aorta	Aorta
2	chr6:44229400-44232800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:44230000-44233200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr6:44230200-44232800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:44230200-44233400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:44230400-44232200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:44230400-44232800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:44230400-44232800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr6:44230400-44232800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:44230400-44232800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:44230400-44232800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr6:44230400-44232800	Flanking Active TSS	HUVEC	blood vessel
13	chr6:44230400-44233000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:44230400-44233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:44230400-44233000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr6:44230400-44233000	Flanking Active TSS	Placenta	Placenta
17	chr6:44230400-44233200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:44230600-44232200	Enhancers	Left Ventricle	heart
19	chr6:44230600-44232400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:44230600-44232400	Enhancers	Ovary	ovary
21	chr6:44230600-44232600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr6:44230600-44232600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:44230600-44232600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:44230600-44232600	Flanking Active TSS	Esophagus	oesophagus
25	chr6:44230600-44232600	Flanking Active TSS	NHEK	skin
26	chr6:44230600-44232800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr6:44230600-44232800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr6:44230600-44232800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr6:44230600-44232800	Flanking Active TSS	HMEC	breast
30	chr6:44230600-44233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr6:44230600-44233000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:44230600-44233000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:44230600-44233000	Flanking Active TSS	Liver	Liver
34	chr6:44230600-44233000	Flanking Active TSS	Colonic Mucosa	Colon
35	chr6:44230600-44233000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr6:44230600-44233000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr6:44230800-44232200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:44230800-44232200	Flanking Active TSS	A549	lung
39	chr6:44230800-44232400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:44230800-44232400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr6:44230800-44232600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:44230800-44232600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr6:44230800-44232600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:44230800-44232600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:44230800-44232800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:44230800-44232800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:44230800-44232800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:44230800-44232800	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr6:44230800-44232800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr6:44230800-44232800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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