Variant report

Variant	rs240375
Chromosome Location	chr6:75994572-75994573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:487)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:487 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:75994480-75994630	BJ	skin:	n/a	n/a
2	FOS	chr6:75994560-75994843	MCF10A-Er-Src	breast:	n/a	n/a
3	REST	chr6:75993833-75995120	H1-neurons	neurons:	n/a	n/a
4	USF1	chr6:75994323-75994913	K562	blood:	n/a	n/a
5	USF1	chr6:75994327-75995014	HCT-116	colon:	n/a	n/a
6	CEBPB	chr6:75994360-75995401	GM12878	blood:	n/a	chr6:75995198-75995215
7	POLR2A	chr6:75994084-75995371	GM15510	blood:	n/a	n/a
8	POLR2A	chr6:75994205-75994941	HCT-116	colon:	n/a	n/a
9	TCF12	chr6:75993986-75995043	ECC-1	luminal epithelium:	n/a	n/a
10	JUND	chr6:75994223-75994757	A549	lung:	n/a	n/a
11	MAX	chr6:75994562-75995005	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr6:75994090-75995082	Hela-S3	cervix:	n/a	n/a
13	IRF1	chr6:75994058-75995666	K562	blood:	n/a	chr6:75994537-75994551 chr6:75995171-75995181 chr6:75995651-75995665 chr6:75995651-75995661 chr6:75994538-75994555
14	ELK1	chr6:75994371-75995431	GM12878	blood:	n/a	n/a
15	CTCF	chr6:75994440-75994590	HRE	kidney:	n/a	n/a
16	GABPA	chr6:75994014-75995067	MCF-7	breast:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
17	MAX	chr6:75993992-75995227	K562	blood:	n/a	n/a
18	NRF1	chr6:75994389-75994904	GM12878	blood:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994712-75994723 chr6:75994710-75994724 chr6:75994713-75994727
19	USF1	chr6:75994424-75994876	A549	lung:	n/a	n/a
20	NFATC1	chr6:75994319-75995317	GM12878	blood:	n/a	n/a
21	ZNF263	chr6:75993583-75995340	HEK293-T-REx	kidney:	n/a	chr6:75994071-75994080 chr6:75994607-75994628 chr6:75994582-75994603
22	CHD2	chr6:75993943-75995329	K562	blood:	n/a	n/a
23	POLR2A	chr6:75993826-75995472	GM19193	blood:	n/a	n/a
24	YY1	chr6:75994178-75994970	GM12892	blood:	n/a	n/a
25	USF1	chr6:75994465-75994855	A549	lung:	n/a	n/a
26	IRF4	chr6:75994292-75995192	GM12878	blood:	n/a	n/a
27	ATF1	chr6:75994470-75995206	K562	blood:	n/a	n/a
28	USF1	chr6:75994191-75995007	HCT-116	colon:	n/a	n/a
29	SIN3AK20	chr6:75994314-75994586	PFSK-1	brain:	n/a	n/a
30	KAP1	chr6:75993808-75995377	HEK293	kidney:	n/a	n/a
31	MAX	chr6:75994161-75995187	MCF-7	breast:	n/a	n/a
32	RFX5	chr6:75994473-75995166	HepG2	liver:	n/a	n/a
33	TCF7L2	chr6:75994252-75994916	PANC-1	pancreas:	n/a	n/a
34	EP300	chr6:75993616-75995335	GM12878	blood:	n/a	chr6:75995145-75995159 chr6:75993959-75993973
35	GABPA	chr6:75994247-75994825	Hela-S3	cervix:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
36	REST	chr6:75994480-75995069	HepG2	liver:	n/a	n/a
37	YY1	chr6:75994421-75994823	A549	lung:	n/a	n/a
38	POLR2A	chr6:75994136-75995072	PANC-1	pancreas:	n/a	n/a
39	SP1	chr6:75994202-75994967	A549	lung:	n/a	chr6:75994501-75994515 chr6:75994619-75994630
40	USF1	chr6:75994419-75994829	SK-N-SH_RA	brain:	n/a	n/a
41	RFX5	chr6:75994426-75994881	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:75994126-75995104	U87	brain:	n/a	n/a
43	RCOR1	chr6:75993947-75994910	HepG2	liver:	n/a	n/a
44	FOXA1	chr6:75994501-75995086	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:75993738-75995279	GM12878	blood:	n/a	n/a
46	CTCF	chr6:75994480-75994630	HMF	breast:	n/a	n/a
47	SIN3AK20	chr6:75994475-75994968	A549	lung:	n/a	n/a
48	USF1	chr6:75994389-75994904	K562	blood:	n/a	n/a
49	TAF1	chr6:75994384-75994958	GM12891	blood:	n/a	n/a
50	TBP	chr6:75994050-75995106	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:75994563-75994613	HEK293	kidney:	embryo
2	chr6:75994563-75994613	U87	brain:	n/a
3	chr6:75994563-75994613	RPTEC	kidney:	n/a
4	chr6:75994563-75994613	NH-A	brain:	n/a
5	chr6:75994563-75994613	HRCEpiC	kidney:	n/a
6	chr6:75994563-75994613	NB4	blood:	n/a
7	chr6:75994563-75994613	ProgFib	skin:	n/a
8	chr6:75994563-75994613	SKMC	muscle:	n/a
9	chr6:75994563-75994613	Hepatocyte	liver:	n/a
10	chr6:75994563-75994613	K562	blood:	n/a
11	chr6:75994563-75994613	HCT-116	colon:	n/a
12	chr6:75994563-75994613	AG04449	skin:	fetal
13	chr6:75994563-75994613	PFSK-1	brain:	n/a
14	chr6:75994563-75994613	GM12891	blood:	n/a
15	chr6:75994563-75994613	GM12892	blood:	n/a
16	chr6:75994563-75994613	AG04450	lung:	fetal
17	chr6:75994563-75994613	HCPEpiC	choroid plexus:	n/a
18	chr6:75994563-75994613	HRPEpiC	eye:	n/a
19	chr6:75994563-75994613	GM12878	blood:	n/a
20	chr6:75994563-75994613	AG10803	skin:	n/a
21	chr6:75994563-75994613	MCF10A-Er-Src	breast:	n/a
22	chr6:75994563-75994613	HCF	heart:	n/a
23	chr6:75994563-75994613	BJ	skin:	n/a
24	chr6:75994563-75994613	Jurkat	blood:	n/a
25	chr6:75994563-75994613	HCM	heart:	n/a
26	chr6:75994563-75994613	NHBE	bronchial:	n/a
27	chr6:75994563-75994613	SK-N-SH_RA	brain:	n/a
28	chr6:75994563-75994613	SK-N-SH	brain:	n/a
29	chr6:75994563-75994613	SAEC	small airway:	n/a
30	chr6:75994563-75994613	HUVEC	blood vessel:	n/a
31	chr6:75994563-75994613	HRE	kidney:	n/a
32	chr6:75994563-75994613	GM06990	blood:	n/a
33	chr6:75994563-75994613	LNCaP	prostate:	n/a
34	chr6:75994563-75994613	HPAEpiC	pulmonary alveolar:	n/a
35	chr6:75994563-75994613	GM19239	blood:	n/a
36	chr6:75994563-75994613	IMR90	lung:	fetal
37	chr6:75994563-75994613	ECC-1	luminal epithelium:	n/a
38	chr6:75994563-75994613	A549	lung:	n/a
39	chr6:75994563-75994613	HIPEpiC	eye:	n/a
40	chr6:75994563-75994613	HepG2	liver:	n/a
41	chr6:75994563-75994613	NT2-D1	testis:	n/a
42	chr6:75994563-75994613	AG09319	gingival:	n/a
43	chr6:75994563-75994613	HAEpiC	amniotic membrane:	n/a
44	chr6:75994563-75994613	AG09309	skin:	n/a
45	chr6:75994563-75994613	PrEC	prostate:	n/a
46	chr6:75994563-75994613	AoSMC	blood vessel:	n/a
47	chr6:75994563-75994613	Hela-S3	cervix:	n/a
48	chr6:75994563-75994613	PANC-1	pancreas:	n/a
49	chr6:75994563-75994613	H1-hESC	embryonic stem cell:	embryo
50	chr6:75994563-75994613	HNPCEpiC	eye:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:75981554..75983680-chr6:75993870..75995991,2	K562	blood:
2	chr6:75951699..75955124-chr6:75992599..75996025,9	K562	blood:
3	chr6:30709897..30710718-chr6:75994395..75995294,2	Hela-S3	cervix:
4	chr4:76597747..76598353-chr6:75994277..75995225,2	Hela-S3	cervix:
5	chr6:75949911..75955499-chr6:75993041..75995715,6	MCF-7	breast:
6	chr6:75993142..75995708-chr6:76310246..76313188,4	K562	blood:
7	chr6:75982180..75984876-chr6:75993848..75995841,3	K562	blood:
8	chr6:75951366..75953542-chr6:75992434..75995845,4	K562	blood:
9	chr6:75951485..75954328-chr6:75992401..75995008,3	MCF-7	breast:
10	chr6:75993176..75995308-chr6:76310710..76312367,2	MCF-7	breast:
11	chr3:59035260..59035930-chr6:75994213..75994894,2	HCT-116	colon:

No data

Variant related genes	Relation type
TMEM30A	TF binding region
ENSG00000225793	TF binding region
ENSG00000225793	CpG island
TMEM30A	CpG island
ENSG00000112701	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000112695	Chromatin interaction
ENSG00000163689	Chromatin interaction
ENSG00000112697	Chromatin interaction
ENSG00000138757	Chromatin interaction
ENSG00000272273	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1018471	0.85[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10806035	0.80[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs171263	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250989	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240378	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240379	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240380	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748252	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2808201	0.83[MEX][hapmap]
rs2808203	0.91[MEX][hapmap]
rs2842446	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842458	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842459	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842462	0.80[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs2842463	0.80[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708179	0.80[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs6903526	0.91[MEX][hapmap]
rs6904580	0.87[MEX][hapmap]
rs6929270	0.91[MEX][hapmap]
rs7743227	0.84[CEU][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7771904	0.91[MEX][hapmap]
rs7772989	0.85[JPT][hapmap]
rs9352202	0.80[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs9359122	0.87[MEX][hapmap]

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	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers 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 miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs240375	TMEM30A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75987800-75996200	Active TSS	GM12878-XiMat	blood
2	chr6:75989200-75995800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:75990000-75995400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:75990200-75996400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:75991000-75996000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:75991000-75996000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:75991200-75995400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:75991200-75995400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:75991400-75995200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:75991400-75995600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:75991400-75995600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:75991400-75995600	Active TSS	HMEC	breast
13	chr6:75991400-75995600	Active TSS	NHLF	lung
14	chr6:75991600-75996000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:75991600-75997000	Active TSS	A549	lung
16	chr6:75991800-75995400	Active TSS	Aorta	Aorta
17	chr6:75991800-75995600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:75991800-75995600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:75991800-75995800	Active TSS	NHDF-Ad	bronchial
20	chr6:75991800-75996400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:75991800-75997600	Active TSS	K562	blood
22	chr6:75992000-75995400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:75992000-75995600	Active TSS	NH-A	brain
24	chr6:75992000-75995800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:75992000-75995800	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr6:75992000-75996400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:75992200-75995400	Active TSS	HSMMtube	muscle
28	chr6:75992400-75995400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:75992400-75995400	Active TSS	Right Ventricle	heart
30	chr6:75992400-75995600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:75992400-75995600	Active TSS	Fetal Kidney	kidney
32	chr6:75992400-75995600	Active TSS	HSMM	muscle
33	chr6:75992600-75995200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:75992600-75995400	Active TSS	Colon Smooth Muscle	Colon
35	chr6:75992600-75995400	Active TSS	Ovary	ovary
36	chr6:75992600-75995600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:75992600-75995800	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr6:75992600-75995800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:75992800-75995200	Active TSS	Brain Hippocampus Middle	brain
40	chr6:75992800-75995200	Active TSS	Left Ventricle	heart
41	chr6:75992800-75995400	Active TSS	H9 Cell Line	embryonic stem cell
42	chr6:75992800-75995400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:75992800-75995400	Active TSS	Colonic Mucosa	Colon
44	chr6:75992800-75995400	Active TSS	Psoas Muscle	Psoas
45	chr6:75992800-75995600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr6:75992800-75995600	Active TSS	Brain Anterior Caudate	brain
47	chr6:75992800-75995600	Active TSS	Duodenum Mucosa	Duodenum
48	chr6:75992800-75995600	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:75992800-75995600	Active TSS	Fetal Intestine Small	intestine
50	chr6:75992800-75995600	Active TSS	Fetal Muscle Leg	muscle

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