Variant report

Variant	rs6438535
Chromosome Location	chr3:119218714-119218715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119218599-119218931	SK-N-SH	brain:	n/a	n/a
2	BHLHE40	chr3:119218278-119218810	K562	blood:	n/a	n/a
3	POLR2A	chr3:119218368-119219001	SK-N-SH	brain:	n/a	n/a
4	USF1	chr3:119218381-119218793	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:119218321-119220778	K562	blood:	n/a	n/a
6	MYC	chr3:119218461-119219000	K562	blood:	n/a	n/a
7	MXI1	chr3:119216044-119220289	SK-N-SH	brain:	n/a	n/a
8	SREBP1	chr3:119216866-119218863	GM12878	blood:	n/a	n/a
9	USF1	chr3:119218323-119218717	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:119218234-119218750	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr3:119216028-119218789	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:119215979-119219829	SK-N-MC	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119218133..119220642-chr3:119277892..119280066,2	K562	blood:
2	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
3	chr3:118957609..118959509-chr3:119217273..119218823,2	MCF-7	breast:
4	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
5	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
6	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
7	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
8	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
9	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
10	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
11	chr3:119217361..119219124-chr3:119394788..119396855,3	MCF-7	breast:
12	chr3:119215904..119218714-chr3:135913674..135916504,2	MCF-7	breast:

No data

Variant related genes	Relation type
TIMMDC1	TF binding region
ENSG00000272662	TF binding region
ENSG00000174579	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000121594	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1060569	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934493	0.85[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs13080905	0.94[ASN][1000 genomes]
rs1797839	0.91[ASN][1000 genomes]
rs1900742	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919586	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919590	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1967621	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976919	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030816	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3814397	0.91[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687860	0.94[ASN][1000 genomes]
rs4688005	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688008	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688012	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688014	0.89[ASN][1000 genomes]
rs6414282	0.91[ASN][1000 genomes]
rs6414283	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6438529	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438530	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438531	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6778945	0.92[ASN][1000 genomes]
rs6794822	0.91[ASN][1000 genomes]
rs6796970	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs727905	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7621259	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628626	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630587	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7642502	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289129	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9809155	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9836326	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9836627	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850447	0.92[ASN][1000 genomes]
rs9867768	0.88[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9873196	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874480	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9877854	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438535	FSTL1	cis	cerebellum	SCAN
rs6438535	CCDC58	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119216000-119218800	Active TSS	NHLF	lung
2	chr3:119216200-119218800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:119216200-119219200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:119216200-119219600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr3:119216200-119219600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:119216200-119219800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:119216200-119220000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:119216400-119218800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:119216400-119219200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:119216400-119219400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:119216400-119219600	Active TSS	Psoas Muscle	Psoas
12	chr3:119216400-119220200	Active TSS	K562	blood
13	chr3:119216600-119218800	Active TSS	Placenta	Placenta
14	chr3:119216600-119218800	Active TSS	HSMM	muscle
15	chr3:119216600-119219000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:119216600-119219800	Active TSS	Left Ventricle	heart
17	chr3:119216800-119218800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr3:119216800-119218800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:119217400-119218800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:119217600-119219000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:119217800-119218800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:119217800-119218800	Flanking Active TSS	Fetal Thymus	thymus
23	chr3:119218000-119218800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:119218000-119218800	Enhancers	Fetal Brain Male	brain
25	chr3:119218000-119219000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:119218000-119219000	Enhancers	Stomach Mucosa	stomach
27	chr3:119218000-119219200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:119218000-119220400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:119218000-119224400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:119218000-119225000	Weak transcription	Gastric	stomach
31	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
33	chr3:119218200-119218800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:119218200-119218800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:119218200-119218800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:119218200-119218800	Flanking Active TSS	Liver	Liver
37	chr3:119218200-119218800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr3:119218200-119219000	Enhancers	Primary B cells from cord blood	blood
39	chr3:119218200-119219000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:119218200-119219000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:119218200-119219000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:119218200-119219000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr3:119218200-119219000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr3:119218200-119219000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr3:119218200-119219000	Flanking Active TSS	NH-A	brain
46	chr3:119218200-119219200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr3:119218200-119219200	Weak transcription	Ovary	ovary
48	chr3:119218200-119219400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:119218200-119219400	Enhancers	Primary hematopoietic stem cells	blood
50	chr3:119218200-119219400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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