Variant report

Variant	rs4240617
Chromosome Location	chr8:8242800-8242801
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	POLR2A	chr8:8241189-8244122	GM12891	blood:	n/a	n/a
2	MXI1	chr8:8242099-8244945	SK-N-SH	brain:	n/a	n/a
3	RUNX3	chr8:8242292-8243247	GM12878	blood:	n/a	n/a
4	CTCF	chr8:8242700-8242850	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr8:8242742-8242950	H1-hESC	embryonic stem cell:	n/a	n/a
6	EBF1	chr8:8242724-8243450	GM12878	blood:	n/a	chr8:8242971-8242984 chr8:8242944-8242955
7	POLR2A	chr8:8241334-8244104	GM12878	blood:	n/a	n/a
8	EBF1	chr8:8242745-8243179	GM12878	blood:	n/a	chr8:8242971-8242984 chr8:8242944-8242955
9	POLR2A	chr8:8242588-8244238	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:8242731-8244153	GM12878	blood:	n/a	n/a
11	CTCF	chr8:8242744-8242805	GM12892	blood:	n/a	n/a
12	BCLAF1	chr8:8242654-8244555	GM12878	blood:	n/a	chr8:8243925-8243938 chr8:8244209-8244218 chr8:8244197-8244210 chr8:8243956-8243969
13	BCLAF1	chr8:8242693-8243303	GM12878	blood:	n/a	n/a
14	MXI1	chr8:8242659-8244128	GM12878	blood:	n/a	n/a
15	POLR2A	chr8:8238700-8244933	HepG2	liver:	n/a	n/a
16	POLR2A	chr8:8242656-8244287	GM18505	blood:	n/a	n/a
17	EP300	chr8:8242766-8242933	HepG2	liver:	n/a	chr8:8242767-8242781 chr8:8242851-8242865
18	TCF12	chr8:8242521-8245145	A549	lung:	n/a	n/a
19	CTCF	chr8:8242720-8242870	AG10803	skin:	n/a	n/a
20	MYC	chr8:8242757-8243470	MCF10A-Er-Src	breast:	n/a	chr8:8242799-8242809
21	RUNX3	chr8:8242638-8243143	GM12878	blood:	n/a	n/a
22	POLR2A	chr8:8242766-8243334	GM12878	blood:	n/a	n/a
23	POLR2A	chr8:8242794-8242818	HepG2	liver:	n/a	n/a
24	POLR2A	chr8:8242794-8243451	HepG2	liver:	n/a	n/a
25	CHD1	chr8:8242678-8243893	H1-hESC	embryonic stem cell:	n/a	chr8:8243099-8243109
26	POLR2A	chr8:8242636-8244327	GM12892	blood:	n/a	n/a
27	MXI1	chr8:8241193-8244764	IMR90	lung:	n/a	n/a
28	MTA3	chr8:8242520-8244041	GM12878	blood:	n/a	n/a
29	CTCF	chr8:8242700-8242850	HCPEpiC	choroid plexus:	n/a	n/a
30	RAD21	chr8:8241177-8244104	IMR90	lung:	n/a	chr8:8243690-8243702 chr8:8241808-8241820 chr8:8243828-8243841 chr8:8241285-8241304
31	RAD21	chr8:8242622-8243678	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr8:8242556-8244906	Hela-S3	cervix:	n/a	chr8:8244212-8244222
33	MYC	chr8:8242796-8243464	MCF10A-Er-Src	breast:	n/a	chr8:8242799-8242809
34	SIN3A	chr8:8241250-8244923	H1-hESC	embryonic stem cell:	n/a	chr8:8244247-8244260 chr8:8241608-8241616 chr8:8244481-8244490 chr8:8244479-8244488
35	POLR2A	chr8:8242800-8242882	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr8:8242605-8245098	A549	lung:	n/a	chr8:8244478-8244486 chr8:8242799-8242809 chr8:8244479-8244490 chr8:8244480-8244489
37	CTCF	chr8:8242711-8242826	GM19239	blood:	n/a	n/a
38	CTCF	chr8:8242740-8242890	HEEpiC	esophagus:	n/a	n/a
39	CHD1	chr8:8241249-8244244	IMR90	lung:	n/a	chr8:8243099-8243109
40	CTCF	chr8:8242740-8242890	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:8242378..8243902-chr8:8594357..8596139,2	MCF-7	breast:
2	chr8:8238437..8240547-chr8:8242096..8244614,4	K562	blood:
3	chr8:8235042..8240063-chr8:8240771..8244973,7	MCF-7	breast:
4	chr8:8233939..8236566-chr8:8240658..8243964,3	K562	blood:
5	chr8:8241927..8245169-chr8:8316549..8319625,5	MCF-7	breast:
6	chr8:8242160..8245521-chr8:8318713..8321604,3	MCF-7	breast:
7	chr8:8240682..8243465-chr8:8266165..8269097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182319	TF binding region
ENSG00000254153	Chromatin interaction
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10089767	0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10097659	0.86[CEU][hapmap];0.80[GIH][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10481460	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12546045	0.83[EUR][1000 genomes]
rs12547958	0.84[EUR][1000 genomes]
rs34628823	0.90[EUR][1000 genomes]
rs35038563	0.90[EUR][1000 genomes]
rs3896980	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3932318	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4840341	0.86[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4840946	0.82[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4840947	0.95[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4840948	0.82[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4840950	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4840951	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4840952	1.00[CEU][hapmap]
rs4840953	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4840955	0.80[EUR][1000 genomes]
rs57583445	0.90[EUR][1000 genomes]
rs7841735	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][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	nsv817196	chr8:8079861-8255544	Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1032259	chr8:8108863-8247113	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1020290	chr8:8108863-8260280	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv539440	chr8:8108863-8260280	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
15	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
17	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4240617	ERI1	cis	parietal	SCAN
rs4240617	DEFB134	cis	cerebellum	SCAN
rs4240617	C8orf12	cis	cerebellum	SCAN
rs4240617	CTSB	cis	cerebellum	SCAN

Chromatin state (count:152 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8238800-8243400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:8239200-8243000	Weak transcription	Spleen	Spleen
3	chr8:8241000-8242800	Flanking Active TSS	Fetal Lung	lung
4	chr8:8241000-8243000	Active TSS	Right Ventricle	heart
5	chr8:8241200-8242800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr8:8241200-8242800	Enhancers	Brain Substantia Nigra	brain
7	chr8:8241200-8242800	Bivalent Enhancer	Fetal Thymus	thymus
8	chr8:8241200-8242800	Enhancers	Stomach Mucosa	stomach
9	chr8:8241200-8242800	Flanking Active TSS	NHEK	skin
10	chr8:8241200-8243000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr8:8241200-8243000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr8:8241200-8243000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr8:8241200-8243200	Active TSS	Right Atrium	heart
14	chr8:8241200-8243400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr8:8241200-8243800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr8:8241200-8244400	Active TSS	NHLF	lung
17	chr8:8241200-8244600	Active TSS	Psoas Muscle	Psoas
18	chr8:8241200-8245000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr8:8241200-8245000	Active TSS	HSMMtube	muscle
20	chr8:8241400-8242800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:8241400-8242800	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr8:8241400-8243000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:8241400-8243000	Enhancers	Pancreas	Pancrea
24	chr8:8241400-8243000	Flanking Active TSS	HUVEC	blood vessel
25	chr8:8241400-8243400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr8:8241400-8243400	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr8:8241400-8243400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:8241400-8243400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr8:8241400-8243600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr8:8241400-8243600	Bivalent/Poised TSS	HepG2	liver
31	chr8:8241400-8244800	Active TSS	Rectal Smooth Muscle	rectum
32	chr8:8241600-8243200	Flanking Active TSS	Hela-S3	cervix
33	chr8:8241600-8243400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:8241600-8243600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr8:8241600-8243800	Flanking Bivalent TSS/Enh	Dnd41	blood
36	chr8:8241600-8244400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr8:8241600-8245000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr8:8241800-8242800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:8241800-8242800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr8:8241800-8242800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr8:8241800-8243000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr8:8241800-8243000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr8:8241800-8243000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
44	chr8:8241800-8243600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr8:8241800-8244200	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr8:8241800-8244200	Active TSS	GM12878-XiMat	blood
47	chr8:8241800-8244400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr8:8241800-8244600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr8:8241800-8244600	Active TSS	A549	lung
50	chr8:8241800-8244800	Active TSS	H1 Cell Line	embryonic stem cell

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