Variant report

Variant	rs12974922
Chromosome Location	chr19:36848604-36848605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36848342..36851339-chr19:37018243..37021228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12974973	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12975337	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12975393	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12976232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12979121	0.85[EUR][1000 genomes]
rs12982193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12983243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16960884	0.81[CEU][hapmap]
rs16970932	0.81[CEU][hapmap]
rs17639717	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34288068	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34386841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34656490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34957973	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35152981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35186959	0.95[EUR][1000 genomes]
rs35338669	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35577694	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35669779	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35778194	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35840887	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951452	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36000557	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs36026111	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4133047	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55825342	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71354192	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71354193	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71354194	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71354195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7247321	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7256914	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259940	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7260462	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8109676	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110644	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8111836	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8113338	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1066190	chr19:36830299-36852877	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv174	chr19:36831719-36865415	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv9716	chr19:36840250-36851177	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3318769	chr19:36844612-36849010	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3318770	chr19:36844612-36849010	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv579453	chr19:36845339-36848604	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv579459	chr19:36845537-36856379	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv579460	chr19:36846000-36850222	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1795509	chr19:36847366-36852733	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36823800-36853600	ZNF genes & repeats	Liver	Liver
2	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:36830600-36869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:36832200-36849600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:36832200-36868600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:36832400-36851400	Weak transcription	Fetal Brain Male	brain
7	chr19:36832600-36849600	Weak transcription	Fetal Heart	heart
8	chr19:36832800-36849000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:36834000-36857400	Weak transcription	Brain Substantia Nigra	brain
10	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:36834400-36849600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:36835800-36857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:36836400-36858400	Weak transcription	Osteobl	bone
15	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
16	chr19:36836600-36849800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:36836600-36849800	Weak transcription	Colonic Mucosa	Colon
18	chr19:36836600-36857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:36836800-36849800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:36837000-36852600	Strong transcription	Fetal Stomach	stomach
22	chr19:36838000-36849600	Weak transcription	Small Intestine	intestine
23	chr19:36838000-36851200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:36838000-36851200	Weak transcription	HepG2	liver
25	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
26	chr19:36838200-36849400	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:36838200-36855000	Weak transcription	HSMM	muscle
28	chr19:36838600-36850400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:36839400-36849600	Weak transcription	Gastric	stomach
30	chr19:36839400-36851200	Weak transcription	HSMMtube	muscle
31	chr19:36839600-36849600	Weak transcription	Pancreas	Pancrea
32	chr19:36839800-36849800	Weak transcription	Spleen	Spleen
33	chr19:36839800-36850600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:36839800-36851200	Weak transcription	Placenta	Placenta
35	chr19:36840000-36849600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:36840000-36849800	Weak transcription	Aorta	Aorta
37	chr19:36840000-36849800	Weak transcription	Esophagus	oesophagus
38	chr19:36840000-36855000	Weak transcription	Right Ventricle	heart
39	chr19:36840000-36856000	Weak transcription	Fetal Lung	lung
40	chr19:36841200-36854800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:36842600-36851600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:36843600-36851000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:36844200-36849000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:36844200-36849400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:36844200-36849800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:36844200-36851000	Weak transcription	Fetal Kidney	kidney
48	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:36844600-36850400	Weak transcription	Fetal Intestine Large	intestine
50	chr19:36845000-36849600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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