Variant report

Variant	rs5742993
Chromosome Location	chr2:190663043-190663044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190648962..190650889-chr2:190662854..190664736,2	MCF-7	breast:
2	chr2:190655757..190657993-chr2:190660819..190663491,2	K562	blood:
3	chr2:190660869..190663581-chr2:191032978..191035653,2	K562	blood:
4	chr2:190662961..190664099-chr2:190934762..190935615,4	MCF-7	breast:
5	chr2:190655142..190657284-chr2:190662768..190665130,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064933	Chromatin interaction
ENSG00000128699	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233267	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233270	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233273	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233274	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233286	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13404927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16831960	0.87[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2544054	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256571	1.00[JPT][hapmap]
rs5742924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742994	0.81[EUR][1000 genomes]
rs5742997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743003	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743048	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743090	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743130	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs5743161	1.00[CEU][hapmap]
rs5743164	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5743169	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5743175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs58147864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60386871	0.82[EUR][1000 genomes]
rs6750293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73042330	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73054335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054339	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735558	0.82[EUR][1000 genomes]
rs7579156	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv3080	chr2:190661654-190706515	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5742993	HBG1	trans	brain	seeQTL
rs5742993	HBG2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
2	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
3	chr2:190649800-190713400	Weak transcription	Gastric	stomach
4	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:190650200-190668200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:190650200-190669200	Weak transcription	Right Ventricle	heart
7	chr2:190650200-190673000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:190650200-190673200	Weak transcription	Small Intestine	intestine
9	chr2:190650400-190664600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:190650400-190666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:190650400-190667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:190650400-190670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:190650400-190675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
15	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
16	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:190650600-190664000	Weak transcription	NHLF	lung
19	chr2:190650600-190668200	Weak transcription	Fetal Brain Female	brain
20	chr2:190650600-190683200	Weak transcription	Fetal Brain Male	brain
21	chr2:190650600-190688800	Weak transcription	Fetal Heart	heart
22	chr2:190650600-190693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
24	chr2:190650800-190675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:190651000-190673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:190651000-190673400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:190651200-190673800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:190653400-190673000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:190655000-190671800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:190656000-190663400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:190656200-190663400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:190656200-190663400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:190656200-190670800	Strong transcription	HepG2	liver
34	chr2:190656200-190673000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:190656200-190677800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:190656400-190663200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:190656400-190665000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:190656600-190663200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:190656800-190663600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:190656800-190664800	Strong transcription	Liver	Liver
41	chr2:190656800-190666600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:190656800-190685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:190657000-190663200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:190657000-190664400	Strong transcription	Dnd41	blood
46	chr2:190657600-190663600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:190657600-190665000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:190657600-190669400	Strong transcription	Fetal Thymus	thymus
49	chr2:190657800-190665000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:190657800-190665000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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