Variant report

Variant	rs947421
Chromosome Location	chr1:70033217-70033218
allele	C/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	REST	chr1:70032603-70036648	H1-neurons	neurons:	n/a	chr1:70034458-70034468 chr1:70033549-70033562 chr1:70034350-70034363
2	HA-E2F1	chr1:70032780-70033468	MCF-7	breast:	n/a	chr1:70032967-70032976
3	HMGN3	chr1:70032823-70033361	K562	blood:	n/a	n/a
4	POLR2A	chr1:70032619-70036444	H1-neurons	neurons:	n/a	n/a
5	ZNF143	chr1:70032835-70033378	H1-hESC	embryonic stem cell:	n/a	chr1:70032967-70032977
6	POLR2A	chr1:70032548-70036420	H1-neurons	neurons:	n/a	n/a
7	MAX	chr1:70032684-70034559	H1-hESC	embryonic stem cell:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
8	RCOR1	chr1:70032820-70033522	K562	blood:	n/a	n/a
9	GATA2	chr1:70032821-70034175	SH-SY5Y	brain:	n/a	chr1:70034157-70034168
10	E2F6	chr1:70032786-70034712	K562	blood:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70033548-70033560 chr1:70033933-70033942
11	CHD2	chr1:70033151-70033387	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr1:70032830-70033498	H1-hESC	embryonic stem cell:	n/a	chr1:70032967-70032977
13	ZNF263	chr1:70032639-70035829	HEK293-T-REx	kidney:	n/a	n/a
14	RAD21	chr1:70032786-70033283	H1-hESC	embryonic stem cell:	n/a	chr1:70033166-70033180
15	TAF1	chr1:70032810-70033821	H1-neurons	neurons:	n/a	n/a
16	E2F6	chr1:70032779-70034603	H1-hESC	embryonic stem cell:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70033548-70033560 chr1:70033933-70033942
17	E2F6	chr1:70032830-70033324	K562	blood:	n/a	chr1:70032967-70032976
18	MAZ	chr1:70032791-70033230	K562	blood:	n/a	chr1:70032967-70032977
19	RCOR1	chr1:70032671-70033530	K562	blood:	n/a	n/a
20	BHLHE40	chr1:70032777-70033381	K562	blood:	n/a	chr1:70033162-70033178
21	E2F6	chr1:70033073-70033282	K562	blood:	n/a	n/a
22	POLR2A	chr1:70032634-70033361	K562	blood:	n/a	n/a
23	MAX	chr1:70032713-70033465	K562	blood:	n/a	chr1:70032967-70032977
24	GABPA	chr1:70032887-70033257	K562	blood:	n/a	chr1:70032967-70032976
25	MAX	chr1:70032966-70034046	ECC-1	luminal epithelium:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
26	POLR2A	chr1:70032771-70033247	K562	blood:	n/a	n/a
27	REST	chr1:70032593-70034195	H1-neurons	neurons:	n/a	chr1:70033549-70033562
28	UBTF	chr1:70032928-70033233	K562	blood:	n/a	n/a
29	SIN3A	chr1:70032685-70033478	H1-hESC	embryonic stem cell:	n/a	chr1:70032826-70032839 chr1:70033172-70033185
30	MAX	chr1:70032701-70033892	H1-hESC	embryonic stem cell:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
31	TAF1	chr1:70032658-70034444	H1-neurons	neurons:	n/a	n/a
32	E2F6	chr1:70032816-70035598	H1-hESC	embryonic stem cell:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70035268-70035277 chr1:70033548-70033560 chr1:70033933-70033942
33	UBTF	chr1:70032788-70033320	K562	blood:	n/a	n/a
34	CCNT2	chr1:70032858-70033331	K562	blood:	n/a	n/a
35	MAX	chr1:70032949-70034065	ECC-1	luminal epithelium:	n/a	chr1:70033546-70033556 chr1:70032967-70032977

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70028289..70031072-chr1:70031175..70033274,4	K562	blood:

Variant related genes	Relation type
LRRC7	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10749793	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10749794	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10889838	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209488	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11209490	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027307	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12063209	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12116687	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119817	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12567881	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12750500	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418013	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1418016	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1592101	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1630201	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4589058	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4650295	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71575482	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529053	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531427	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537519	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537706	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539145	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830126	chr1:70014879-70167979	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70031800-70034200	Active TSS	Fetal Brain Female	brain
2	chr1:70032000-70034000	Active TSS	Brain Hippocampus Middle	brain
3	chr1:70032000-70036400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:70032200-70036800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:70032200-70038400	Active TSS	Brain Anterior Caudate	brain
6	chr1:70032400-70033600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:70032400-70033600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:70032400-70033600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr1:70032400-70034800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:70032400-70035000	Active TSS	Psoas Muscle	Psoas
11	chr1:70032400-70035200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
12	chr1:70032400-70035600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:70032400-70035600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:70032400-70036400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:70032400-70036400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr1:70032400-70036400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr1:70032400-70036400	Active TSS	Brain Cingulate Gyrus	brain
18	chr1:70032400-70036600	Active TSS	Brain Angular Gyrus	brain
19	chr1:70032400-70036600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:70032600-70033400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:70032600-70033400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr1:70032600-70033400	Flanking Active TSS	HMEC	breast
23	chr1:70032600-70033600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:70032600-70033600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:70032600-70033600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:70032600-70033600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr1:70032600-70033600	Active TSS	Brain Germinal Matrix	brain
28	chr1:70032600-70033600	Active TSS	Esophagus	oesophagus
29	chr1:70032600-70033600	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr1:70032600-70033800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:70032600-70033800	Active TSS	Fetal Heart	heart
32	chr1:70032600-70033800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
33	chr1:70032600-70033800	Active TSS	Rectal Smooth Muscle	rectum
34	chr1:70032600-70033800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
35	chr1:70032600-70034000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:70032600-70034000	Bivalent/Poised TSS	NH-A	brain
37	chr1:70032600-70034000	Bivalent/Poised TSS	NHDF-Ad	bronchial
38	chr1:70032600-70034200	Flanking Active TSS	HUVEC	blood vessel
39	chr1:70032600-70034400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:70032600-70034400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr1:70032600-70034400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
42	chr1:70032600-70034600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr1:70032600-70034600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:70032600-70034600	Active TSS	Fetal Kidney	kidney
45	chr1:70032600-70034600	Active TSS	K562	blood
46	chr1:70032600-70035000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:70032600-70035200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr1:70032600-70035200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
49	chr1:70032600-70035400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:70032600-70035600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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