Variant report

Variant	rs11185538
Chromosome Location	chr3:196149667-196149668
allele	C/T
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	GATA3	chr3:196149654-196149824	SH-SY5Y	brain:	n/a	n/a
2	NFIC	chr3:196149663-196150249	ECC-1	luminal epithelium:	n/a	n/a
3	MXI1	chr3:196149435-196150745	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196123859..196126007-chr3:196148082..196150188,2	MCF-7	breast:
2	chr3:196146851..196150238-chr3:196157711..196160603,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226345	TF binding region
ENSG00000225822	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000241868	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11185525	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs11185536	0.82[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11707862	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715772	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718924	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487829	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770487	0.85[ASN][1000 genomes]
rs6770643	0.85[ASN][1000 genomes]
rs6799210	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
8	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
14	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
16	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
2	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:196127000-196153800	Weak transcription	NHEK	skin
5	chr3:196127400-196152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:196127600-196157400	Weak transcription	HUVEC	blood vessel
7	chr3:196128000-196149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:196132200-196153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:196132400-196150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:196132600-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:196132600-196157400	Weak transcription	Liver	Liver
12	chr3:196134000-196149800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:196134000-196150000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:196134000-196152600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:196134000-196153800	Weak transcription	Primary B cells from cord blood	blood
16	chr3:196134000-196154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:196134200-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:196134200-196153800	Weak transcription	Hela-S3	cervix
19	chr3:196134200-196154600	Weak transcription	Dnd41	blood
20	chr3:196134200-196157400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:196134400-196150400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:196134600-196157800	Weak transcription	A549	lung
23	chr3:196136000-196149800	Weak transcription	Fetal Lung	lung
24	chr3:196136600-196150000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:196136600-196156800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:196136800-196149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:196137000-196149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:196137000-196153000	Weak transcription	Thymus	Thymus
29	chr3:196137200-196149800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:196138200-196156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:196138200-196157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:196138400-196153000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:196139000-196150000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:196139400-196154000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:196141600-196157400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:196141600-196158000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:196142000-196149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:196142000-196149800	Weak transcription	Osteobl	bone
39	chr3:196142000-196152000	Weak transcription	Primary T cells from cord blood	blood
40	chr3:196142000-196157400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:196143200-196149800	Weak transcription	Spleen	Spleen
42	chr3:196143200-196150200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:196143400-196149800	Weak transcription	Ovary	ovary
44	chr3:196143600-196149800	Weak transcription	Adipose Nuclei	Adipose
45	chr3:196143600-196157400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:196143800-196150200	Weak transcription	HepG2	liver
47	chr3:196144000-196149800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:196144200-196154000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:196144400-196151600	Enhancers	Fetal Heart	heart
50	chr3:196144600-196149800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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