Variant report

Variant	rs16994684
Chromosome Location	chr19:19717451-19717452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19717080..19720260-chr19:19736721..19739619,3	MCF-7	breast:
2	chr19:19716730..19718451-chr19:19737365..19740401,3	MCF-7	breast:
3	chr19:19717211..19719147-chr19:19729115..19731402,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CILP2-1	chr19:19716690-19717574	ENSG00000259242.1
2	lnc-CILP2-1	chr19:19717159-19717574	ENSG00000259242.2

Variant related genes	Relation type
ENSG00000105717	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10403759	1.00[ASN][1000 genomes]
rs10411387	1.00[ASW][hapmap]
rs10426732	1.00[ASW][hapmap]
rs11878202	0.98[ASN][1000 genomes]
rs11879838	0.95[ASN][1000 genomes]
rs12971734	1.00[CEU][hapmap]
rs12974308	0.83[EUR][1000 genomes]
rs12976582	0.83[EUR][1000 genomes]
rs12976826	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982049	0.83[EUR][1000 genomes]
rs1433079	0.83[EUR][1000 genomes]
rs16996174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968047	0.96[ASN][1000 genomes]
rs2033481	1.00[CEU][hapmap];0.95[GIH][hapmap]
rs2043293	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34558847	0.83[EUR][1000 genomes]
rs34725331	0.98[ASN][1000 genomes]
rs35035906	0.83[EUR][1000 genomes]
rs35445661	0.83[EUR][1000 genomes]
rs35449009	0.83[EUR][1000 genomes]
rs35792080	0.83[EUR][1000 genomes]
rs3752152	0.83[EUR][1000 genomes]
rs3794996	0.80[EUR][1000 genomes]
rs4808974	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252228	0.98[ASN][1000 genomes]
rs739461	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs74181147	0.83[EUR][1000 genomes]
rs74181148	0.83[EUR][1000 genomes]
rs74181149	0.83[EUR][1000 genomes]
rs74181150	0.83[EUR][1000 genomes]
rs74181151	0.83[EUR][1000 genomes]
rs8101679	0.99[ASN][1000 genomes]
rs8113682	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs880090	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19702600-19719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19706600-19728200	Weak transcription	Fetal Brain Male	brain
3	chr19:19707000-19718600	Weak transcription	Fetal Lung	lung
4	chr19:19707600-19728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:19708800-19720000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:19708800-19724400	Weak transcription	NHDF-Ad	bronchial
7	chr19:19709000-19719200	Weak transcription	Fetal Brain Female	brain
8	chr19:19710200-19718800	Weak transcription	Fetal Stomach	stomach
9	chr19:19712800-19719400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:19712800-19724400	Weak transcription	Gastric	stomach
11	chr19:19713200-19719400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:19713600-19718600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:19713800-19718400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:19713800-19719200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:19713800-19728000	Weak transcription	Brain Germinal Matrix	brain
16	chr19:19714000-19728800	Weak transcription	Brain Anterior Caudate	brain
17	chr19:19714200-19724400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:19716200-19717600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:19716200-19718600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:19716400-19717800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr19:19716600-19717600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:19716600-19717600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr19:19716600-19717600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:19716600-19718000	Enhancers	Primary T cells from cord blood	blood
25	chr19:19716600-19718000	Enhancers	Hela-S3	cervix
26	chr19:19716600-19720000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19716800-19717600	Enhancers	Dnd41	blood
28	chr19:19716800-19717800	Flanking Active TSS	Fetal Thymus	thymus
29	chr19:19716800-19718400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr19:19717000-19717600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:19717000-19717600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:19717000-19717600	Enhancers	Spleen	Spleen
33	chr19:19717000-19717800	Enhancers	Fetal Muscle Trunk	muscle
34	chr19:19717200-19717600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr19:19717200-19717600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:19717200-19717600	Flanking Active TSS	Stomach Mucosa	stomach
37	chr19:19717200-19719400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:19717200-19724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:19717400-19717600	Enhancers	Duodenum Mucosa	Duodenum
40	chr19:19717400-19717600	Enhancers	Thymus	Thymus
41	chr19:19717400-19718600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr19:19717400-19718800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr19:19717400-19718800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:19717400-19719200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:19717400-19719400	Weak transcription	HSMMtube	muscle
46	chr19:19717400-19719600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:19717400-19721200	Weak transcription	Placenta	Placenta
48	chr19:19717400-19721400	Weak transcription	GM12878-XiMat	blood
49	chr19:19717400-19721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:19717400-19724200	Weak transcription	Fetal Muscle Leg	muscle

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