Variant report

Variant	rs709400
Chromosome Location	chr14:104149475-104149476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:104149271-104150107	K562	blood:	n/a	n/a
2	POLR2A	chr14:104149407-104150017	U87	brain:	n/a	n/a
3	POLR2A	chr14:104149428-104149682	K562	blood:	n/a	n/a
4	POLR2A	chr14:104149468-104150011	U87	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XRCC3-1	chr14:104149195-104150352	ENSG00000246451
2	lnc-XRCC3-1	chr14:104149195-104150352	ENSG00000246451

Variant related genes	Relation type
KLC1	TF binding region
ENSG00000270108	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10134399	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs10135248	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10143623	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10145755	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10147049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149249	0.91[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap]
rs11622552	0.83[JPT][hapmap]
rs11624505	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11627794	0.83[ASN][1000 genomes]
rs11849259	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2274268	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs2403205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3915733	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864158	0.81[AFR][1000 genomes]
rs55885592	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56660916	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57218990	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58133129	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61995780	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6593	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68087451	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7150141	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7154948	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs7359090	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7693	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs8003090	0.88[AFR][1000 genomes]
rs8005885	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8018979	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs861528	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs861531	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs861534	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs861536	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]
rs861538	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs861539	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs861548	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942863	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs709400	DNAH8	trans	parietal	SCAN
rs709400	C14orf153	cis	parietal	SCAN
rs709400	DIO3	cis	cerebellum	SCAN
rs709400	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs709400	APOPT1	cis	Muscle Skeletal	GTEx
rs709400	BAG5	cis	multi-tissue	Pritchard
rs709400	KLC1	cis	parietal	SCAN
rs709400	ZFYVE21	cis	cerebellum	SCAN
rs709400	MARK3	cis	Thyroid	GTEx
rs709400	BAG5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:104117800-104157000	Strong transcription	Dnd41	blood
3	chr14:104117800-104176000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:104118800-104175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:104119200-104155600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:104119200-104173000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:104119400-104157000	Strong transcription	Fetal Thymus	thymus
8	chr14:104119400-104161800	Strong transcription	Fetal Intestine Small	intestine
9	chr14:104119400-104164600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr14:104119400-104175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr14:104120000-104177000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr14:104120200-104149800	Strong transcription	Fetal Muscle Leg	muscle
13	chr14:104120200-104155000	Strong transcription	Fetal Brain Female	brain
14	chr14:104120200-104161400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:104120200-104161800	Strong transcription	Fetal Intestine Large	intestine
16	chr14:104120400-104150000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr14:104120400-104157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr14:104120400-104157000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr14:104120400-104161200	Strong transcription	Fetal Stomach	stomach
20	chr14:104120600-104155000	Strong transcription	Brain Germinal Matrix	brain
21	chr14:104120800-104157200	Strong transcription	Thymus	Thymus
22	chr14:104121000-104154200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr14:104121000-104154800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr14:104121000-104162000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:104122800-104153000	Strong transcription	Liver	Liver
26	chr14:104123400-104155200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:104124600-104169800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr14:104124600-104169800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr14:104125200-104155400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:104130400-104153000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:104130600-104149800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:104130600-104150400	Strong transcription	Adipose Nuclei	Adipose
33	chr14:104130600-104159600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr14:104130800-104155600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr14:104131000-104161800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr14:104131400-104155200	Strong transcription	Brain Anterior Caudate	brain
37	chr14:104132000-104155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:104132200-104154800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr14:104132800-104156000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:104133400-104177200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:104133800-104150400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr14:104133800-104153600	Strong transcription	Osteobl	bone
43	chr14:104133800-104154800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr14:104133800-104157000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr14:104134000-104152400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr14:104134000-104153400	Strong transcription	NH-A	brain
47	chr14:104134000-104154800	Strong transcription	NHEK	skin
48	chr14:104134000-104156400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr14:104134000-104157000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr14:104134000-104157000	Strong transcription	Primary T cells from cord blood	blood

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