Variant report

Variant	rs35343040
Chromosome Location	chr3:48641971-48641972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48641470-48642834	K562	blood:	n/a	n/a
2	POLR2A	chr3:48641690-48642773	K562	blood:	n/a	n/a
3	POLR2A	chr3:48641635-48643121	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48641673..48644998-chr3:48670911..48673807,4	K562	blood:
2	chr3:48639116..48644270-chr3:48645185..48648761,6	K562	blood:
3	chr3:48640950..48644386-chr3:48644481..48647187,5	MCF-7	breast:
4	chr3:48637650..48639338-chr3:48640052..48642052,2	MCF-7	breast:
5	chr3:48591611..48596652-chr3:48640512..48642956,4	MCF-7	breast:

No data

Variant related genes	Relation type
UQCRC1	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1003649	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10470687	0.85[ASN][1000 genomes]
rs13060933	0.86[ASN][1000 genomes]
rs13063312	0.83[ASN][1000 genomes]
rs13076269	0.81[ASN][1000 genomes]
rs13096357	0.81[ASN][1000 genomes]
rs13319635	0.86[ASN][1000 genomes]
rs13319651	0.86[ASN][1000 genomes]
rs13324142	0.81[ASN][1000 genomes]
rs17080289	0.98[ASN][1000 genomes]
rs2276850	0.83[ASN][1000 genomes]
rs2276852	0.83[ASN][1000 genomes]
rs2310996	0.86[ASN][1000 genomes]
rs2310997	0.81[ASN][1000 genomes]
rs2854394	0.92[ASN][1000 genomes]
rs2854395	0.92[ASN][1000 genomes]
rs28563843	0.80[ASN][1000 genomes]
rs28581474	0.94[ASN][1000 genomes]
rs34368826	0.83[ASN][1000 genomes]
rs35562294	0.85[ASN][1000 genomes]
rs35796820	0.98[ASN][1000 genomes]
rs3755819	0.85[ASN][1000 genomes]
rs3806694	0.83[ASN][1000 genomes]
rs3821876	0.81[ASN][1000 genomes]
rs57334642	0.83[ASN][1000 genomes]
rs6773261	0.81[ASN][1000 genomes]
rs6781283	0.86[ASN][1000 genomes]
rs6792156	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792525	0.85[ASN][1000 genomes]
rs740787	0.86[ASN][1000 genomes]
rs7620853	0.86[ASN][1000 genomes]
rs7631574	0.86[ASN][1000 genomes]
rs9810549	0.80[ASN][1000 genomes]
rs9810991	0.80[ASN][1000 genomes]
rs9830581	1.00[ASN][1000 genomes]
rs9837687	0.80[ASN][1000 genomes]
rs9843316	1.00[ASN][1000 genomes]
rs9848824	0.80[ASN][1000 genomes]
rs9849280	0.80[ASN][1000 genomes]
rs9864729	0.80[ASN][1000 genomes]
rs9869698	0.80[ASN][1000 genomes]
rs9871180	0.83[ASN][1000 genomes]
rs9878063	0.83[ASN][1000 genomes]
rs9878950	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9881877	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48634000-48642400	Strong transcription	Fetal Brain Female	brain
2	chr3:48634200-48644200	Strong transcription	Brain Germinal Matrix	brain
3	chr3:48634200-48644600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:48634200-48646200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:48634400-48643400	Strong transcription	Primary B cells from cord blood	blood
6	chr3:48634400-48643600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:48634600-48644000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:48634600-48644400	Strong transcription	Primary T cells from cord blood	blood
9	chr3:48634600-48645200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:48634600-48645200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:48634600-48645600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:48634600-48645600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48634600-48645600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:48634600-48645800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:48634800-48643600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:48634800-48643600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:48634800-48643600	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48634800-48643600	Strong transcription	Thymus	Thymus
19	chr3:48634800-48644000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:48634800-48644000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:48634800-48645600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr3:48634800-48645600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:48634800-48645600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:48635000-48643600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:48635000-48643600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:48635000-48643600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:48635000-48644000	Strong transcription	Dnd41	blood
28	chr3:48635000-48644400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:48635000-48644400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:48635000-48645600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:48635000-48645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:48635000-48645600	Strong transcription	Fetal Intestine Large	intestine
33	chr3:48635200-48643600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:48635200-48643600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:48635200-48643600	Strong transcription	Liver	Liver
36	chr3:48635200-48643600	Strong transcription	Brain Substantia Nigra	brain
37	chr3:48635200-48643800	Strong transcription	Brain Anterior Caudate	brain
38	chr3:48635200-48644000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:48635400-48644000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:48635400-48644000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr3:48635600-48643400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:48635600-48645600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48636000-48643200	Strong transcription	HepG2	liver
44	chr3:48636000-48643800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:48636000-48643800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:48636200-48643600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:48636200-48643600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:48636200-48645400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:48636400-48643400	Strong transcription	Adipose Nuclei	Adipose
50	chr3:48636400-48644000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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