Variant report

Variant	rs17621388
Chromosome Location	chr14:39839469-39839470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39572245..39573793-chr14:39838003..39840919,2	MCF-7	breast:
2	chr14:39570993..39573887-chr14:39839322..39841759,2	MCF-7	breast:
3	chr14:39698483..39701019-chr14:39836995..39839487,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-407N17.3.1-2	chr14:39839079-39839679	NONHSAT036532

Variant related genes	Relation type
ENSG00000150526	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000258651	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10137623	0.87[CHB][hapmap]
rs1056345	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs11560068	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12891025	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12891299	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570131	0.82[JPT][hapmap]
rs17692639	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs17694832	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955704	0.81[AFR][1000 genomes]
rs2148507	0.87[AFR][1000 genomes]
rs2415542	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2415546	0.87[CHB][hapmap]
rs28464878	0.82[ASN][1000 genomes]
rs34173090	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34594880	0.80[EUR][1000 genomes]
rs34651350	0.81[AFR][1000 genomes]
rs34654496	0.81[AFR][1000 genomes]
rs34843498	0.83[CHB][hapmap]
rs34983854	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35026953	0.81[AFR][1000 genomes]
rs35690918	0.81[AFR][1000 genomes]
rs35869816	0.81[EUR][1000 genomes]
rs36090203	0.81[AFR][1000 genomes]
rs4531652	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56127968	0.81[AFR][1000 genomes]
rs7143942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7149971	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs7154632	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7155164	0.84[JPT][hapmap]
rs72675474	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8006182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8014839	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8015094	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8017737	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8020472	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8020596	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
3	chr14:39792800-39841600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr14:39794400-39843200	Weak transcription	HUVEC	blood vessel
5	chr14:39802000-39841200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:39803000-39845800	Weak transcription	NHEK	skin
7	chr14:39803200-39843400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:39803200-39845800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr14:39803400-39843800	Weak transcription	HMEC	breast
10	chr14:39808400-39841200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr14:39812200-39845800	Weak transcription	Stomach Mucosa	stomach
12	chr14:39816800-39843200	Weak transcription	Hela-S3	cervix
13	chr14:39816800-39850200	Weak transcription	Fetal Kidney	kidney
14	chr14:39817400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:39818800-39845200	Weak transcription	Placenta	Placenta
16	chr14:39818800-39867200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr14:39826000-39843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:39833800-39839600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:39833800-39841400	Weak transcription	Osteobl	bone
20	chr14:39834000-39851600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr14:39834400-39839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:39834600-39846000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr14:39834600-39851600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr14:39834800-39840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:39834800-39846000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:39835000-39841000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr14:39835000-39851600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr14:39835200-39851600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr14:39835400-39840600	Strong transcription	Fetal Intestine Large	intestine
30	chr14:39835400-39851400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr14:39835400-39872400	Weak transcription	Fetal Muscle Leg	muscle
32	chr14:39836000-39839600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr14:39836000-39845600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr14:39836200-39872800	Weak transcription	Esophagus	oesophagus
35	chr14:39836400-39839600	Weak transcription	Pancreas	Pancrea
36	chr14:39836400-39839800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr14:39836400-39870600	Weak transcription	Gastric	stomach
38	chr14:39836600-39839600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr14:39836600-39843400	Weak transcription	NH-A	brain
40	chr14:39836600-39845800	Weak transcription	Right Atrium	heart
41	chr14:39836600-39852600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr14:39836800-39839600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:39836800-39845800	Weak transcription	Brain Anterior Caudate	brain
44	chr14:39836800-39845800	Weak transcription	Right Ventricle	heart
45	chr14:39837000-39852600	Weak transcription	Primary T cells from cord blood	blood
46	chr14:39837400-39839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:39837600-39839600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:39837600-39839600	Weak transcription	Brain Substantia Nigra	brain
49	chr14:39837600-39845800	Weak transcription	Brain Angular Gyrus	brain
50	chr14:39837600-39845800	Weak transcription	Colon Smooth Muscle	Colon

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