Variant report

Variant	rs17187553
Chromosome Location	chr6:30026164-30026165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30023200..30024877-chr6:30024886..30026414,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30026145-30026524	ENSG00000204623
2	lnc-RNF39-4	chr6:30026145-30028756	ENSG00000204623

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17180528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17186951	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187658	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187826	1.00[EUR][1000 genomes]
rs17187847	1.00[EUR][1000 genomes]
rs17194258	1.00[EUR][1000 genomes]
rs3888631	1.00[ASN][1000 genomes]
rs4713289	1.00[EUR][1000 genomes]
rs4959042	1.00[EUR][1000 genomes]
rs55945512	1.00[ASN][1000 genomes]
rs56908820	1.00[EUR][1000 genomes]
rs57303436	1.00[ASN][1000 genomes]
rs59812435	1.00[ASN][1000 genomes]
rs6906435	1.00[AMR][1000 genomes]
rs6917420	1.00[EUR][1000 genomes]
rs73725925	1.00[ASN][1000 genomes]
rs73725942	1.00[ASN][1000 genomes]
rs73725957	1.00[ASN][1000 genomes]
rs73725968	1.00[ASN][1000 genomes]
rs73727658	1.00[ASN][1000 genomes]
rs7740741	1.00[EUR][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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
8	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
10	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
11	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
14	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
16	chr6:30003000-30027200	Weak transcription	Dnd41	blood
17	chr6:30006200-30027600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:30011000-30027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:30012400-30027400	Weak transcription	HepG2	liver
20	chr6:30012600-30027200	Weak transcription	HMEC	breast
21	chr6:30012600-30027800	Weak transcription	Small Intestine	intestine
22	chr6:30012800-30027600	Weak transcription	NHDF-Ad	bronchial
23	chr6:30012800-30027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:30012800-30027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:30013000-30027400	Weak transcription	NHEK	skin
26	chr6:30013000-30027400	Weak transcription	NHLF	lung
27	chr6:30013000-30027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30013400-30027600	Weak transcription	NH-A	brain
29	chr6:30013600-30027600	Weak transcription	Hela-S3	cervix
30	chr6:30013600-30027800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:30013600-30027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30013800-30027200	Weak transcription	GM12878-XiMat	blood
33	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:30015600-30027400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:30015600-30027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:30016000-30027800	Weak transcription	Spleen	Spleen
37	chr6:30016800-30027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:30017000-30027600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:30017400-30028400	Weak transcription	Lung	lung
40	chr6:30018000-30027600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:30018800-30027200	Weak transcription	Osteobl	bone
42	chr6:30020000-30027800	Weak transcription	Fetal Stomach	stomach
43	chr6:30020200-30027600	Weak transcription	HUVEC	blood vessel
44	chr6:30020200-30027800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:30020400-30028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr6:30020800-30026200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:30021400-30026200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:30021400-30026400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:30021400-30026600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:30021400-30027400	Weak transcription	A549	lung

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