Variant report

Variant	rs6761553
Chromosome Location	chr2:144995566-144995567
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	ELF1	chr2:144995449-144995786	K562	blood:	n/a	n/a
2	YY1	chr2:144995319-144995759	GM12892	blood:	n/a	n/a
3	YY1	chr2:144995394-144995765	GM12878	blood:	n/a	n/a
4	JUND	chr2:144995393-144995747	K562	blood:	n/a	n/a
5	SPI1	chr2:144995464-144996296	HL-60	blood:	n/a	n/a
6	POLR2A	chr2:144995326-144996203	HL-60	blood:	n/a	n/a
7	YY1	chr2:144995452-144995716	K562	blood:	n/a	n/a
8	FOXA2	chr2:144995371-144995612	HepG2	liver:	n/a	n/a
9	WRNIP1	chr2:144995351-144995763	GM12878	blood:	n/a	n/a
10	FOXA1	chr2:144995359-144995615	HepG2	liver:	n/a	n/a
11	YY1	chr2:144995373-144995774	GM12878	blood:	n/a	n/a
12	YY1	chr2:144995390-144995714	GM12892	blood:	n/a	n/a
13	FOXA1	chr2:144995372-144995644	T-47D	breast:	n/a	n/a
14	YY1	chr2:144995398-144995734	GM12891	blood:	n/a	n/a
15	FOXA1	chr2:144995303-144995689	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16823571	0.81[LWK][hapmap];0.90[MKK][hapmap];1.00[AMR][1000 genomes]
rs16823579	0.81[LWK][hapmap];0.93[MKK][hapmap]
rs16823594	1.00[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16823596	1.00[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs16823598	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16823607	1.00[AMR][1000 genomes]
rs16823609	1.00[MKK][hapmap]
rs16823684	1.00[AMR][1000 genomes]
rs16823718	1.00[AMR][1000 genomes]
rs60695751	1.00[AMR][1000 genomes]
rs72992123	1.00[AMR][1000 genomes]
rs72992134	1.00[AMR][1000 genomes]
rs72992136	1.00[AMR][1000 genomes]
rs72992138	1.00[AMR][1000 genomes]
rs73008262	1.00[AMR][1000 genomes]
rs73008283	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv834396	chr2:144842187-145019465	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6761553	LOC96610	trans	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144962600-144998600	Weak transcription	Psoas Muscle	Psoas
2	chr2:144964400-144998200	Weak transcription	Fetal Kidney	kidney
3	chr2:144965400-145010000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:144985400-144998400	Weak transcription	Small Intestine	intestine
5	chr2:144988200-144998600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:144988800-144998000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:144991000-144997200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:144991200-144998200	Weak transcription	Adipose Nuclei	Adipose
9	chr2:144991200-144998400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:144992400-144998600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:144992400-145000000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:144992600-144995600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:144992600-144997400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:144992600-144998200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:144992800-144996800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:144992800-144997000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:144992800-144997000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:144992800-144997000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:144992800-144997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:144992800-144997000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:144992800-144997000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:144992800-144997200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:144992800-144997200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:144992800-144997200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:144992800-144997600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:144992800-144998000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:144992800-144998200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:144992800-144998400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:144992800-144998600	Weak transcription	Brain Germinal Matrix	brain
30	chr2:144993000-144996200	Enhancers	Fetal Lung	lung
31	chr2:144993000-144997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:144993200-144998200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:144993800-144998400	Weak transcription	Fetal Brain Male	brain
34	chr2:144993800-144998800	Weak transcription	Fetal Brain Female	brain
35	chr2:144994400-144995800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:144994600-144995600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:144994600-144995800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:144994600-144995800	Enhancers	K562	blood
39	chr2:144994600-145000800	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:144994800-144996200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:144994800-144996800	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:144994800-144998200	Enhancers	GM12878-XiMat	blood
43	chr2:144995000-144996200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:144995200-144995600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:144995200-144995600	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:144995200-144995600	Enhancers	Left Ventricle	heart
47	chr2:144995200-144995600	Enhancers	Lung	lung
48	chr2:144995200-144995600	Enhancers	Thymus	Thymus
49	chr2:144995200-144995600	Enhancers	Spleen	Spleen
50	chr2:144995200-144995600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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