Variant report

Variant	rs4617878
Chromosome Location	chr16:30791463-30791464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30789931..30791663-chr16:30816269..30818821,2	K562	blood:
2	chr16:30536813..30539768-chr16:30790008..30791588,2	K562	blood:
3	chr16:30717636..30719490-chr16:30791065..30792593,2	MCF-7	breast:
4	chr16:30783772..30791593-chr16:30931071..30936822,9	MCF-7	breast:
5	chr16:30784974..30791554-chr16:30930641..30936449,8	MCF-7	breast:
6	chr16:30749452..30756542-chr16:30785692..30792123,12	MCF-7	breast:
7	chr16:30707557..30712450-chr16:30785751..30791890,10	K562	blood:
8	chr16:30789931..30792790-chr16:30816269..30820303,5	K562	blood:
9	chr16:30787489..30791955-chr16:30902887..30909666,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF40-1	chr16:30789770-30791473	ENSG00000262026.1

No data

Variant related genes	Relation type
ENSG00000150281	Chromatin interaction
ENSG00000099385	Chromatin interaction
ENSG00000260899	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000262721	Chromatin interaction
ENSG00000211591	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000099364	Chromatin interaction
ENSG00000260852	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10782000	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11150594	1.00[AMR][1000 genomes]
rs11150595	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap]
rs11648654	1.00[AMR][1000 genomes]
rs12596375	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[AMR][1000 genomes]
rs12596394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12598056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12931844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12933849	1.00[AMR][1000 genomes]
rs1530203	1.00[ASW][hapmap];0.80[MKK][hapmap]
rs1550477	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053426	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099754	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099755	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2919427	0.89[ASW][hapmap]
rs2919429	0.87[ASW][hapmap]
rs2919430	1.00[AMR][1000 genomes]
rs2919431	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919432	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919433	1.00[AMR][1000 genomes]
rs2972804	1.00[AMR][1000 genomes]
rs2972815	1.00[AMR][1000 genomes]
rs4007812	0.80[AFR][1000 genomes]
rs4268760	0.88[AFR][1000 genomes]
rs4889488	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889494	1.00[AMR][1000 genomes]
rs4889500	0.87[ASW][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889501	1.00[AMR][1000 genomes]
rs4889503	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889504	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889505	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889507	0.88[AFR][1000 genomes]
rs4889508	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889509	1.00[ASW][hapmap];0.90[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap]
rs4889510	1.00[AMR][1000 genomes]
rs4889528	1.00[AMR][1000 genomes]
rs55635617	1.00[AMR][1000 genomes]
rs56038936	1.00[AMR][1000 genomes]
rs56209507	1.00[AMR][1000 genomes]
rs57225118	1.00[AMR][1000 genomes]
rs57643871	1.00[AMR][1000 genomes]
rs57877247	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6565203	1.00[AMR][1000 genomes]
rs6565204	1.00[AMR][1000 genomes]
rs6565205	1.00[AMR][1000 genomes]
rs6565208	0.87[ASW][hapmap];1.00[AMR][1000 genomes]
rs6565209	1.00[AMR][1000 genomes]
rs6565210	1.00[AMR][1000 genomes]
rs71380412	0.88[AFR][1000 genomes]
rs7185136	0.87[ASW][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs7188077	0.89[ASW][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7193412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7194763	1.00[AMR][1000 genomes]
rs7195583	0.87[ASW][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7195612	1.00[AMR][1000 genomes]
rs73524581	1.00[AMR][1000 genomes]
rs73524584	1.00[AMR][1000 genomes]
rs73536457	1.00[AMR][1000 genomes]
rs73536466	1.00[AMR][1000 genomes]
rs73536474	1.00[AMR][1000 genomes]
rs73536488	1.00[AMR][1000 genomes]
rs73536498	1.00[AMR][1000 genomes]
rs73536499	1.00[AMR][1000 genomes]
rs8045293	0.85[AFR][1000 genomes]
rs8045484	1.00[ASW][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap]
rs8045550	1.00[AMR][1000 genomes]
rs8045624	1.00[ASW][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8046609	1.00[AMR][1000 genomes]
rs8047743	1.00[AMR][1000 genomes]
rs8048656	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs8049589	1.00[AMR][1000 genomes]
rs8050578	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs8056105	0.96[AFR][1000 genomes]
rs8058475	1.00[AMR][1000 genomes]
rs893926	0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893927	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9319586	0.80[AFR][1000 genomes]
rs9921630	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926855	0.85[AFR][1000 genomes]
rs9934046	1.00[AMR][1000 genomes]
rs9941201	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs9941300	0.87[ASW][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];1.00[AMR][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	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers 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	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
11	nsv9438	chr16:30770203-30799442	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh 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	52 gene(s)	inside rSNPs	diseases
12	nsv905732	chr16:30788182-30837210	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30787600-30793000	Weak transcription	Esophagus	oesophagus
2	chr16:30787600-30793400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:30787600-30797600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:30787800-30792800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:30787800-30793000	Weak transcription	Brain Anterior Caudate	brain
6	chr16:30787800-30793000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:30787800-30793000	Weak transcription	Thymus	Thymus
8	chr16:30787800-30793800	Weak transcription	Brain Substantia Nigra	brain
9	chr16:30787800-30794400	Weak transcription	Primary T cells from cord blood	blood
10	chr16:30787800-30797200	Weak transcription	HMEC	breast
11	chr16:30787800-30797200	Weak transcription	HUVEC	blood vessel
12	chr16:30787800-30797400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr16:30787800-30797400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:30788200-30791800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:30788200-30792000	Weak transcription	Primary B cells from cord blood	blood
16	chr16:30788200-30792000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr16:30788200-30792200	Weak transcription	NHEK	skin
18	chr16:30788200-30793200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:30788200-30793200	Weak transcription	Aorta	Aorta
20	chr16:30788200-30793400	Weak transcription	Brain Angular Gyrus	brain
21	chr16:30788200-30793400	Weak transcription	Fetal Lung	lung
22	chr16:30788200-30796800	Weak transcription	Fetal Brain Male	brain
23	chr16:30788200-30797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr16:30788400-30792200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr16:30788400-30792200	Weak transcription	NH-A	brain
26	chr16:30788400-30792400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:30788400-30793000	Weak transcription	Fetal Thymus	thymus
28	chr16:30788400-30793000	Weak transcription	A549	lung
29	chr16:30788400-30793400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr16:30788400-30793400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:30788400-30796200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr16:30788600-30791800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr16:30788600-30793400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr16:30788600-30793400	Weak transcription	NHDF-Ad	bronchial
35	chr16:30788600-30796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:30788800-30791800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr16:30788800-30791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr16:30788800-30792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:30788800-30792200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr16:30788800-30792400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr16:30788800-30792800	Weak transcription	Colon Smooth Muscle	Colon
42	chr16:30788800-30793000	Weak transcription	Small Intestine	intestine
43	chr16:30789000-30791800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr16:30789000-30793000	Weak transcription	Gastric	stomach
45	chr16:30789000-30793000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr16:30789200-30791800	Weak transcription	Lung	lung
47	chr16:30789200-30793000	Weak transcription	Left Ventricle	heart
48	chr16:30789200-30793200	Weak transcription	Colonic Mucosa	Colon
49	chr16:30789200-30793200	Weak transcription	Dnd41	blood
50	chr16:30789400-30793000	Weak transcription	Ovary	ovary

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