Variant report

Variant	rs1804478
Chromosome Location	chr1:155979033-155979034
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	MAFK	chr1:155978649-155979060	IMR90	lung:	n/a	chr1:155978870-155978885
2	CTCF	chr1:155978960-155979110	SK-N-SH_RA	brain:	n/a	n/a
3	MAFK	chr1:155978639-155979057	HepG2	liver:	n/a	chr1:155978870-155978885
4	MAFF	chr1:155978487-155979048	K562	blood:	n/a	chr1:155978869-155978887
5	MAFK	chr1:155978685-155979059	K562	blood:	n/a	chr1:155978870-155978885
6	POLR2A	chr1:155978174-155979633	PFSK-1	brain:	n/a	n/a
7	MAFK	chr1:155978691-155979063	HepG2	liver:	n/a	chr1:155978870-155978885
8	SP1	chr1:155978802-155979545	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr1:155978490-155979070	Hela-S3	cervix:	n/a	chr1:155978870-155978885 chr1:155978506-155978516
10	CTCF	chr1:155978920-155979070	HepG2	liver:	n/a	n/a
11	MAFF	chr1:155978692-155979062	HepG2	liver:	n/a	chr1:155978869-155978887
12	CTCF	chr1:155978960-155979110	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155977756..155980066-chr1:155982576..155985568,2	MCF-7	breast:
2	chr1:155978414..155980525-chr1:156022299..156025180,2	K562	blood:
3	chr1:155977027..155979132-chr1:156029472..156031221,2	MCF-7	breast:
4	chr1:155906562..155909421-chr1:155978385..155980354,2	K562	blood:
5	chr1:155978402..155979208-chr1:155990515..155991136,2	MCF-7	breast:
6	chr1:155978931..155981805-chr1:155987502..155989827,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGEF2-3	chr1:155978840-155979184	NONHSAT006793

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000132698	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000116586	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10158536	1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10752614	1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796957	1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs10908487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264415	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11264418	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs12080245	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095373	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12138913	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16837075	0.80[YRI][hapmap]
rs16837089	0.86[LWK][hapmap];0.90[YRI][hapmap]
rs4661096	1.00[TSI][hapmap]
rs6674865	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6687169	1.00[GIH][hapmap];1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1804478	HBG1	trans	brain	seeQTL
rs1804478	HBG2	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155973800-155989400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155975400-155979200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:155975600-155979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:155975600-155980400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:155976000-155989600	Strong transcription	Fetal Stomach	stomach
6	chr1:155976200-155988800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:155976600-155982400	Strong transcription	Spleen	Spleen
8	chr1:155976600-155985000	Strong transcription	Lung	lung
9	chr1:155976600-155985400	Strong transcription	Thymus	Thymus
10	chr1:155976600-155988400	Strong transcription	Liver	Liver
11	chr1:155976600-155988400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:155976600-155988600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:155976600-155988800	Strong transcription	Fetal Intestine Small	intestine
14	chr1:155976600-155989200	Strong transcription	Fetal Intestine Large	intestine
15	chr1:155976600-155989400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:155976800-155985000	Strong transcription	Fetal Brain Female	brain
17	chr1:155976800-155985400	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:155976800-155989400	Strong transcription	Fetal Thymus	thymus
19	chr1:155976800-155989600	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:155977000-155980400	Weak transcription	Fetal Brain Male	brain
21	chr1:155977200-155983400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:155977200-155987000	Weak transcription	Fetal Heart	heart
23	chr1:155977200-155989200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:155978000-155983800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:155978200-155979200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:155978200-155979200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:155978200-155980000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:155978200-155982200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:155978200-155982200	Strong transcription	Esophagus	oesophagus
30	chr1:155978200-155982200	Strong transcription	Pancreas	Pancrea
31	chr1:155978200-155983400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:155978200-155983400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:155978200-155985000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:155978200-155985000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:155978200-155985000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:155978200-155985000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:155978200-155985000	Strong transcription	Brain Substantia Nigra	brain
38	chr1:155978200-155985000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:155978200-155985200	Strong transcription	Aorta	Aorta
40	chr1:155978200-155985400	Strong transcription	Adipose Nuclei	Adipose
41	chr1:155978200-155985400	Strong transcription	NHLF	lung
42	chr1:155978200-155986000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:155978200-155987000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr1:155978200-155988200	Strong transcription	Colon Smooth Muscle	Colon
45	chr1:155978200-155988200	Strong transcription	Left Ventricle	heart
46	chr1:155978200-155988600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:155978200-155989000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:155978200-155989200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:155978200-155989200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:155978200-155989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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