Variant report

Variant	rs6960603
Chromosome Location	chr7:140772399-140772400
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	CTCF	chr7:140772360-140772510	HBMEC	blood vessel:	n/a	n/a
2	JUND	chr7:140772344-140772481	HepG2	liver:	n/a	chr7:140772369-140772378
3	POLR2A	chr7:140771018-140773527	H1-neurons	neurons:	n/a	n/a
4	MAX	chr7:140772240-140772857	H1-hESC	embryonic stem cell:	n/a	chr7:140772629-140772639
5	SUZ12	chr7:140771587-140774962	NT2-D1	testis:	n/a	n/a
6	CTCF	chr7:140772340-140772490	GM12865	blood:	n/a	n/a
7	SIN3A	chr7:140772289-140775006	H1-hESC	embryonic stem cell:	n/a	chr7:140773094-140773108 chr7:140773740-140773753 chr7:140773058-140773069 chr7:140773093-140773103 chr7:140773554-140773563
8	POLR2A	chr7:140772236-140772740	MCF-7	breast:	n/a	n/a
9	POLR2A	chr7:140770956-140773536	H1-neurons	neurons:	n/a	n/a
10	TAF1	chr7:140772287-140772508	SK-N-SH	brain:	n/a	n/a
11	HA-E2F1	chr7:140772050-140774780	MCF-7	breast:	n/a	chr7:140774533-140774540 chr7:140773926-140773935 chr7:140774707-140774714 chr7:140774707-140774714 chr7:140774707-140774715 chr7:140773818-140773830 chr7:140773846-140773856 chr7:140774707-140774714 chr7:140774707-140774715
12	MAX	chr7:140772095-140773565	MCF-7	breast:	n/a	chr7:140772629-140772639
13	KAP1	chr7:140771845-140772585	U2OS	brain:	n/a	n/a
14	MXI1	chr7:140770407-140777072	SK-N-SH	brain:	n/a	chr7:140771395-140771410 chr7:140776410-140776425 chr7:140771837-140771846 chr7:140776412-140776427
15	CTCF	chr7:140772351-140772475	LNCaP	prostate:	n/a	n/a
16	POLR2A	chr7:140772242-140772867	MCF-7	breast:	n/a	n/a
17	TBP	chr7:140772334-140772611	HepG2	liver:	n/a	n/a
18	CTCF	chr7:140772382-140772492	MCF-7	breast:	n/a	n/a
19	POLR2A	chr7:140772345-140772582	Gliobla	brain:	n/a	n/a
20	HDAC2	chr7:140772197-140773489	MCF-7	breast:	n/a	n/a
21	RAD21	chr7:140769977-140775280	SK-N-SH	brain:	n/a	chr7:140773885-140773898 chr7:140771224-140771231 chr7:140771067-140771079 chr7:140773552-140773566 chr7:140771222-140771241 chr7:140771227-140771239 chr7:140771067-140771077 chr7:140773739-140773751
22	CTCF	chr7:140772360-140772510	HCPEpiC	choroid plexus:	n/a	n/a
23	KAP1	chr7:140771781-140772610	HEK293	kidney:	n/a	n/a
24	MAX	chr7:140772164-140774788	H1-hESC	embryonic stem cell:	n/a	chr7:140773816-140773826 chr7:140772629-140772639
25	CTCF	chr7:140772360-140772510	SK-N-SH_RA	brain:	n/a	n/a
26	MYC	chr7:140772321-140772487	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr7:140772148-140773065	H1-neurons	neurons:	n/a	n/a
28	REST	chr7:140770782-140777023	H1-neurons	neurons:	n/a	chr7:140773089-140773109 chr7:140773634-140773644 chr7:140772481-140772491 chr7:140773070-140773083 chr7:140772636-140772654 chr7:140773089-140773109 chr7:140774009-140774022 chr7:140773737-140773750 chr7:140773148-140773161 chr7:140773095-140773109 chr7:140773090-140773108 chr7:140773094-140773103
29	CTCF	chr7:140772380-140772530	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr7:140772221-140772528	ProgFib	skin:	n/a	n/a
31	REST	chr7:140772369-140772599	SK-N-SH	brain:	n/a	chr7:140772481-140772491
32	POLR2A	chr7:140770953-140772830	SK-N-MC	brain:	n/a	n/a
33	CTCF	chr7:140772340-140772490	AG09319	gingival:	n/a	n/a
34	ZNF263	chr7:140771693-140772717	HEK293-T-REx	kidney:	n/a	chr7:140772586-140772595
35	REST	chr7:140772392-140772677	H1-hESC	embryonic stem cell:	n/a	chr7:140772481-140772491 chr7:140772636-140772654
36	ATF2	chr7:140771918-140772666	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr7:140771085-140772891	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr7:140772152-140775102	H1-hESC	embryonic stem cell:	n/a	n/a
39	REST	chr7:140772220-140773615	HL-60	blood:	n/a	chr7:140773089-140773109 chr7:140772481-140772491 chr7:140773070-140773083 chr7:140772636-140772654 chr7:140773089-140773109 chr7:140773148-140773161 chr7:140773095-140773109 chr7:140773090-140773108 chr7:140773094-140773103
40	TBP	chr7:140771039-140773265	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr7:140772239-140772575	SK-N-MC	brain:	n/a	n/a
42	REST	chr7:140772109-140772837	H1-neurons	neurons:	n/a	chr7:140772481-140772491 chr7:140772636-140772654
43	JUND	chr7:140771804-140772518	H1-hESC	embryonic stem cell:	n/a	chr7:140772369-140772378
44	CTCF	chr7:140772360-140772510	HPF	lung:	n/a	n/a
45	RAD21	chr7:140772330-140772570	H1-hESC	embryonic stem cell:	n/a	n/a
46	E2F6	chr7:140772310-140773591	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD1	chr7:140771650-140772883	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr7:140770576-140775176	SK-N-SH	brain:	n/a	chr7:140773402-140773410 chr7:140773812-140773825 chr7:140770603-140770611 chr7:140771226-140771234 chr7:140771221-140771239 chr7:140773850-140773863 chr7:140771223-140771244 chr7:140771222-140771238
49	MAX	chr7:140772057-140772652	SK-N-SH	brain:	n/a	chr7:140772629-140772639
50	BACH1	chr7:140772218-140772709	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:140726381..140728137-chr7:140770810..140773677,2	MCF-7	breast:
2	chr7:140770942..140773181-chr7:140930215..140932967,2	MCF-7	breast:
3	chr7:140714581..140715382-chr7:140772383..140773295,2	MCF-7	breast:
4	chr7:140712784..140717043-chr7:140770770..140775163,8	MCF-7	breast:
5	chr7:140713242..140716757-chr7:140770540..140776348,9	MCF-7	breast:

Variant related genes	Relation type
TMEM178B	TF binding region
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11762357	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1860752	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2365575	0.85[ASN][1000 genomes]
rs4726263	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491554	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498933	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511001	0.96[ASN][1000 genomes]
rs534348	0.96[ASN][1000 genomes]
rs536809	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553046	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55949610	0.89[ASN][1000 genomes]
rs560981	0.89[ASN][1000 genomes]
rs6464278	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6464330	0.85[ASN][1000 genomes]
rs6944492	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6962233	0.89[ASN][1000 genomes]
rs6967482	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs722219	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7778658	0.88[ASN][1000 genomes]
rs7794979	0.82[AMR][1000 genomes]
rs7805034	0.89[ASN][1000 genomes]
rs7806026	0.89[ASN][1000 genomes]
rs7810146	0.85[ASN][1000 genomes]
rs801157	0.96[ASN][1000 genomes]
rs801158	0.96[ASN][1000 genomes]
rs9640323	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889248	chr7:140754785-140809205	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3417140	chr7:140768130-140783190	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6960603	TMEM178B	cis	Esophagus Mucosa	GTEx
rs6960603	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140770600-140777000	Active TSS	Fetal Brain Female	brain
2	chr7:140770800-140772400	Active TSS	Brain Germinal Matrix	brain
3	chr7:140770800-140774600	Active TSS	Brain Anterior Caudate	brain
4	chr7:140770800-140775600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:140770800-140776800	Active TSS	Brain Cingulate Gyrus	brain
6	chr7:140771000-140772400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:140771000-140772400	Enhancers	Lung	lung
8	chr7:140771000-140772400	Enhancers	Spleen	Spleen
9	chr7:140771000-140772400	Flanking Bivalent TSS/Enh	NHEK	skin
10	chr7:140771000-140772600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
11	chr7:140771000-140773000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
12	chr7:140771000-140773000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:140771000-140773000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
14	chr7:140771000-140773000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
15	chr7:140771000-140773000	Bivalent/Poised TSS	NHLF	lung
16	chr7:140771000-140773200	Active TSS	Colon Smooth Muscle	Colon
17	chr7:140771000-140773400	Bivalent Enhancer	Liver	Liver
18	chr7:140771000-140774000	Bivalent Enhancer	Placenta	Placenta
19	chr7:140771000-140774200	Active TSS	Psoas Muscle	Psoas
20	chr7:140771000-140774600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:140771000-140774600	Active TSS	Brain Angular Gyrus	brain
22	chr7:140771000-140774600	Active TSS	Brain Hippocampus Middle	brain
23	chr7:140771000-140774600	Active TSS	Rectal Smooth Muscle	rectum
24	chr7:140771000-140774800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:140771000-140774800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:140771000-140774800	Active TSS	Brain Substantia Nigra	brain
27	chr7:140771000-140774800	Bivalent/Poised TSS	Thymus	Thymus
28	chr7:140771000-140774800	Bivalent/Poised TSS	HSMM	muscle
29	chr7:140771000-140775000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:140771000-140775200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr7:140771000-140775200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr7:140771000-140775200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr7:140771000-140777000	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr7:140771000-140777000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:140771200-140772400	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:140771200-140772400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
37	chr7:140771200-140772400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
38	chr7:140771200-140772400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
39	chr7:140771200-140772400	Bivalent Enhancer	Fetal Heart	heart
40	chr7:140771200-140772400	Flanking Bivalent TSS/Enh	A549	lung
41	chr7:140771200-140772800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr7:140771200-140772800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:140771200-140772800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
44	chr7:140771200-140773000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr7:140771200-140773200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
46	chr7:140771200-140774600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:140771200-140774800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:140771200-140775000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:140771200-140775000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:140771200-140775200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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