Variant report

Variant	rs861536
Chromosome Location	chr14:104167564-104167565
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	chr14:104094584..104096859-chr14:104165203..104168753,3	MCF-7	breast:
2	chr14:103986573..103988930-chr14:104167446..104169282,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-73M18.2.1-4	chr14:104167538-104167881	NONHSAT040200

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction
ENSG00000166165	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10134399	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs10135248	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10143623	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10145755	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10147049	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10149249	0.91[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap]
rs11624505	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11849259	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2274268	0.88[CEU][hapmap]
rs2403205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3783404	1.00[CEU][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3915733	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55864158	0.81[AFR][1000 genomes]
rs55885592	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56660916	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57218990	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58133129	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61995780	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6593	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68087451	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs709400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7150141	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7154948	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs7359090	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7693	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs8003090	0.88[AFR][1000 genomes]
rs8005885	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8018979	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs861531	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs861534	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861538	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861539	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861548	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs942863	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
12	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv1041347	chr14:104141217-104186372	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
14	nsv902309	chr14:104143385-104198251	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv902310	chr14:104143385-104205811	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
16	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
17	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
18	nsv902311	chr14:104148339-104205811	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
19	nsv902312	chr14:104155317-104211180	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	esv1796914	chr14:104159882-104181369	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
21	nsv527425	chr14:104162263-104198251	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
22	nsv470673	chr14:104162263-104219949	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
23	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
24	nsv902314	chr14:104163901-104170465	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv902315	chr14:104165927-104190527	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs861536	DNAH8	trans	parietal	SCAN
rs861536	ZFYVE21	cis	cerebellum	SCAN
rs861536	C14orf153	cis	parietal	SCAN
rs861536	BAG5	cis	cerebellum	SCAN
rs861536	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs861536	DIO3	cis	cerebellum	SCAN
rs861536	BAG5	cis	multi-tissue	Pritchard
rs861536	KLC1	cis	parietal	SCAN
rs861536	APOPT1	cis	Muscle Skeletal	GTEx
rs861536	MARK3	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104117800-104176000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr14:104118800-104175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr14:104119200-104173000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr14:104119400-104175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr14:104120000-104177000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr14:104124600-104169800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr14:104124600-104169800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr14:104133400-104177200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr14:104135600-104177600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:104146200-104174800	Weak transcription	K562	blood
11	chr14:104152600-104178600	Weak transcription	Small Intestine	intestine
12	chr14:104157400-104167600	Genic enhancers	Placenta	Placenta
13	chr14:104158200-104169000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr14:104158200-104170200	Genic enhancers	Fetal Muscle Leg	muscle
15	chr14:104158400-104167800	Strong transcription	Primary T cells from cord blood	blood
16	chr14:104158400-104171200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr14:104158400-104178000	Strong transcription	Dnd41	blood
18	chr14:104158600-104176400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr14:104159800-104176200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:104161000-104170600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr14:104161000-104176600	Genic enhancers	Spleen	Spleen
22	chr14:104161200-104180000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr14:104161200-104180400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr14:104161800-104167800	Genic enhancers	Right Ventricle	heart
25	chr14:104162000-104169600	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr14:104162400-104172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr14:104162800-104177200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:104163200-104169000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:104163400-104172600	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr14:104163400-104176800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr14:104163400-104177200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:104163600-104176200	Strong transcription	Osteobl	bone
33	chr14:104163600-104177200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr14:104163600-104177600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr14:104163800-104167600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:104163800-104169200	Weak transcription	HUVEC	blood vessel
37	chr14:104163800-104169400	Weak transcription	NH-A	brain
38	chr14:104163800-104169800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr14:104163800-104176200	Strong transcription	Fetal Brain Female	brain
40	chr14:104164000-104167800	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr14:104164000-104169000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:104164000-104170600	Genic enhancers	Adipose Nuclei	Adipose
43	chr14:104164000-104171800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr14:104164000-104172000	Weak transcription	Fetal Kidney	kidney
45	chr14:104164000-104176000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr14:104164000-104176600	Strong transcription	Brain Germinal Matrix	brain
47	chr14:104164200-104175200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr14:104164200-104176800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr14:104164200-104178600	Weak transcription	Fetal Heart	heart
50	chr14:104164400-104167600	Genic enhancers	Brain Inferior Temporal Lobe	brain

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