Variant report

Variant	rs7553830
Chromosome Location	chr1:193035857-193035858
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	ARID3A	chr1:193035445-193036156	K562	blood:	n/a	n/a
2	RCOR1	chr1:193035828-193036113	K562	blood:	n/a	n/a
3	IRF1	chr1:193035432-193036090	K562	blood:	n/a	chr1:193035955-193035968 chr1:193035955-193035969 chr1:193035955-193035966 chr1:193035953-193035967
4	UBTF	chr1:193035739-193035886	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:193033762..193041249-chr1:193071629..193075233,8	K562	blood:
2	chr1:193020543..193046917-chr1:193069266..193098746,125	K562	blood:
3	chr1:193035123..193037127-chr1:193042609..193044640,2	K562	blood:
4	chr1:193035173..193037682-chr1:193044708..193047101,2	MCF-7	breast:
5	chr1:193018810..193043703-chr1:193079188..193098601,93	K562	blood:
6	chr1:193035246..193037642-chr1:193037758..193040535,5	K562	blood:

Variant related genes	Relation type
TROVE2	TF binding region
ENSG00000134371	Chromatin interaction
ENSG00000023572	Chromatin interaction
ENSG00000116747	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16835204	1.00[MEX][hapmap]
rs34552619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34615282	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55842934	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56199152	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58479385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6671794	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6682435	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap]
rs6683844	0.91[YRI][hapmap]
rs6687899	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130911	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130913	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130914	0.85[AMR][1000 genomes]
rs74130916	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130917	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130918	0.85[AMR][1000 genomes]
rs7522932	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs7556154	1.00[MEX][hapmap]
rs7556241	1.00[MEX][hapmap]
rs842806	1.00[MEX][hapmap]
rs842808	1.00[MEX][hapmap]

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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7553830	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193029400-193038400	Weak transcription	Lung	lung
2	chr1:193029400-193040000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:193029400-193046400	Weak transcription	Gastric	stomach
4	chr1:193029400-193051800	Weak transcription	Esophagus	oesophagus
5	chr1:193029400-193051800	Weak transcription	Pancreas	Pancrea
6	chr1:193029800-193046400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:193030000-193046800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:193030200-193046000	Weak transcription	Thymus	Thymus
9	chr1:193030400-193038000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:193030400-193038200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:193030400-193038200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:193030400-193038400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:193030400-193038400	Weak transcription	Fetal Thymus	thymus
14	chr1:193030400-193039000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:193030400-193039600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:193030400-193040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:193030400-193040000	Weak transcription	Psoas Muscle	Psoas
18	chr1:193030400-193040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:193030400-193045000	Weak transcription	Placenta	Placenta
20	chr1:193030400-193045200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:193030400-193046400	Weak transcription	Fetal Stomach	stomach
22	chr1:193030400-193046400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:193030400-193051600	Weak transcription	Colonic Mucosa	Colon
24	chr1:193030600-193038000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:193030600-193038200	Weak transcription	Adipose Nuclei	Adipose
26	chr1:193030600-193038400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:193030600-193039200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:193030600-193039400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:193030600-193039600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:193030600-193040000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:193030600-193040000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:193030600-193046200	Weak transcription	Fetal Kidney	kidney
33	chr1:193030600-193048200	Weak transcription	Fetal Intestine Small	intestine
34	chr1:193030800-193036200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:193030800-193037400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:193030800-193037600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:193030800-193038000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:193030800-193038200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:193030800-193038200	Weak transcription	Liver	Liver
40	chr1:193030800-193038200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:193030800-193038400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:193030800-193038400	Weak transcription	NHEK	skin
43	chr1:193030800-193039800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:193030800-193040200	Weak transcription	NH-A	brain
45	chr1:193030800-193042000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:193030800-193042000	Weak transcription	Fetal Lung	lung
47	chr1:193030800-193042400	Weak transcription	Hela-S3	cervix
48	chr1:193030800-193045400	Weak transcription	NHDF-Ad	bronchial
49	chr1:193030800-193045600	Weak transcription	NHLF	lung
50	chr1:193030800-193045800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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