Variant report

Variant	rs730127
Chromosome Location	chr14:66213465-66213466
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	chr14:65879004..65881155-chr14:66213120..66215142,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2014B16.3.1-4	chr14:66213366-66213869	NONHSAT037395

Variant related genes	Relation type
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10083328	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10131727	1.00[CEU][hapmap]
rs10138701	1.00[TSI][hapmap]
rs10151521	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11845391	0.85[EUR][1000 genomes]
rs11846051	0.85[EUR][1000 genomes]
rs11846827	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11847101	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11849249	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11849408	1.00[CEU][hapmap]
rs11849792	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12432422	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12432550	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12435971	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12436381	1.00[CEU][hapmap]
rs17102760	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17102783	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17102845	0.83[EUR][1000 genomes]
rs17102894	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102898	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17102910	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2268965	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28402125	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28489447	0.81[AMR][1000 genomes]
rs28583930	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28666667	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2898701	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4343192	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs55853120	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56182635	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59036531	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61987768	0.85[EUR][1000 genomes]
rs61987770	0.85[EUR][1000 genomes]
rs61987773	0.85[EUR][1000 genomes]
rs61987776	0.85[EUR][1000 genomes]
rs61987778	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61987779	0.85[EUR][1000 genomes]
rs61987781	0.85[EUR][1000 genomes]
rs61987809	0.88[EUR][1000 genomes]
rs61987810	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61987811	0.85[EUR][1000 genomes]
rs61987812	0.88[EUR][1000 genomes]
rs61987814	0.85[EUR][1000 genomes]
rs61987815	0.88[EUR][1000 genomes]
rs61988019	0.81[EUR][1000 genomes]
rs61988021	0.85[EUR][1000 genomes]
rs61988022	0.85[EUR][1000 genomes]
rs6573620	1.00[CEU][hapmap]
rs7143525	0.85[EUR][1000 genomes]
rs7144234	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7148883	0.85[EUR][1000 genomes]
rs7153718	1.00[CEU][hapmap]
rs7154526	0.85[EUR][1000 genomes]
rs7154876	0.85[EUR][1000 genomes]
rs7155055	1.00[CEU][hapmap]
rs7155169	0.83[EUR][1000 genomes]
rs7342545	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs74056820	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8004852	0.85[EUR][1000 genomes]
rs8019214	1.00[CEU][hapmap]
rs927005	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs956582	0.80[ASW][hapmap];1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs997794	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
2	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1045000	chr14:66010886-66372518	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1042671	chr14:66010886-66399888	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66190400-66217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr14:66191800-66217800	Weak transcription	Small Intestine	intestine
3	chr14:66193000-66218800	Weak transcription	Colonic Mucosa	Colon
4	chr14:66199200-66213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:66200600-66215600	Weak transcription	Brain Substantia Nigra	brain
6	chr14:66201200-66216400	Weak transcription	Fetal Thymus	thymus
7	chr14:66201800-66219200	Weak transcription	Brain Anterior Caudate	brain
8	chr14:66202200-66215000	Weak transcription	Psoas Muscle	Psoas
9	chr14:66207400-66215400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:66209400-66214800	Weak transcription	Primary B cells from cord blood	blood
11	chr14:66209400-66215000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:66209400-66217400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr14:66209400-66217600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:66209400-66219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:66209600-66213800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr14:66209600-66213800	Weak transcription	Ovary	ovary
17	chr14:66209600-66214600	Weak transcription	HSMMtube	muscle
18	chr14:66209600-66215200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:66209600-66216600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:66209600-66217800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr14:66209600-66217800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:66209600-66219000	Weak transcription	Thymus	Thymus
23	chr14:66209600-66219200	Weak transcription	Stomach Mucosa	stomach
24	chr14:66210600-66217400	Weak transcription	GM12878-XiMat	blood
25	chr14:66210600-66217800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr14:66210800-66217400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr14:66211000-66218000	Weak transcription	Fetal Intestine Large	intestine
28	chr14:66211800-66217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:66212000-66213800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr14:66212200-66213600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr14:66212400-66217800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:66212600-66217800	Weak transcription	HepG2	liver
33	chr14:66212800-66214400	Strong transcription	Primary T cells from cord blood	blood
34	chr14:66213200-66213800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:66213400-66214400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr14:66213400-66218000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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