Variant report

Variant	rs11850979
Chromosome Location	chr14:104096558-104096559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104040559..104042718-chr14:104094686..104097466,2	K562	blood:
2	chr14:104092649..104097026-chr14:104179930..104185119,7	MCF-7	breast:
3	chr14:104047041..104049916-chr14:104095707..104097301,2	MCF-7	breast:
4	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
5	chr14:104095098..104097162-chr14:104179460..104182190,3	K562	blood:
6	chr14:104095841..104097584-chr14:104162172..104164814,2	MCF-7	breast:
7	chr14:104093558..104096899-chr14:104170639..104176222,7	MCF-7	breast:
8	chr14:104093419..104097122-chr14:104180603..104183015,4	K562	blood:
9	chr14:104095140..104096884-chr14:104158687..104161252,3	MCF-7	breast:
10	chr14:104091773..104098220-chr14:104179036..104183968,10	MCF-7	breast:
11	chr14:104094844..104097550-chr17:58154950..58156929,2	MCF-7	breast:
12	chr14:104094584..104096859-chr14:104165203..104168753,3	MCF-7	breast:
13	chr14:104096516..104099228-chr14:104099460..104101440,3	K562	blood:
14	chr14:103986778..103989691-chr14:104095238..104098302,4	K562	blood:
15	chr14:104093231..104097862-chr14:104156769..104161796,10	MCF-7	breast:
16	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:
17	chr14:104095744..104098387-chr14:104161337..104163963,2	K562	blood:
18	chr14:104094760..104097289-chr14:104157296..104159578,3	K562	blood:
19	chr14:104092924..104097008-chr14:104171636..104177946,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264904	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000256053	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000269910	Chromatin interaction
ENSG00000269958	Chromatin interaction
ENSG00000224997	Chromatin interaction
ENSG00000269963	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000267416	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000269940	Chromatin interaction
ENSG00000068097	Chromatin interaction
ENSG00000166170	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10047805	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10131067	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1054080	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1078756	0.81[ASN][1000 genomes]
rs11160754	0.83[ASN][1000 genomes]
rs11160756	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11625397	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs11626589	0.81[ASN][1000 genomes]
rs12434218	0.81[JPT][hapmap]
rs12435399	0.81[ASN][1000 genomes]
rs12881418	0.83[JPT][hapmap]
rs12897511	0.87[ASN][1000 genomes]
rs2296483	0.87[JPT][hapmap];0.91[MEX][hapmap]
rs2403202	0.82[CEU][hapmap]
rs2403203	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28798508	0.81[ASN][1000 genomes]
rs28823639	0.81[ASN][1000 genomes]
rs2896489	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212136	0.83[JPT][hapmap]
rs35015260	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35686878	0.85[ASN][1000 genomes]
rs3742463	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3742465	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];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759586	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4318144	0.88[ASN][1000 genomes]
rs4374097	0.81[ASN][1000 genomes]
rs4383078	0.81[ASN][1000 genomes]
rs4444269	0.81[ASN][1000 genomes]
rs4561394	0.91[ASN][1000 genomes]
rs4900583	0.86[ASN][1000 genomes]
rs4900584	0.86[ASN][1000 genomes]
rs4900586	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4900587	0.83[JPT][hapmap]
rs4900589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906340	0.81[ASN][1000 genomes]
rs4906341	0.80[ASN][1000 genomes]
rs4906342	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4906348	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906349	0.87[ASN][1000 genomes]
rs4906352	0.81[ASN][1000 genomes]
rs4906355	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4906358	0.84[EUR][1000 genomes]
rs61436277	0.87[ASN][1000 genomes]
rs61995761	0.80[ASN][1000 genomes]
rs709399	0.80[EUR][1000 genomes]
rs7145234	0.81[ASN][1000 genomes]
rs7154572	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7155511	0.88[ASN][1000 genomes]
rs7156832	0.90[ASN][1000 genomes]
rs7157116	0.80[ASN][1000 genomes]
rs7161125	0.81[ASN][1000 genomes]
rs729437	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745079	0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs752624	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs8003289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007489	0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.81[ASN][1000 genomes]
rs8007903	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs8007915	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8008451	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];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018214	0.90[ASN][1000 genomes]
rs8021368	0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs8021904	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs861530	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs861537	0.91[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs861544	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs861545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs861547	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs8702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	esv3490243	chr14:104083248-104099394	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
9	esv3490244	chr14:104083248-104099394	Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11850979	XRCC3	cis	lymphoblastoid	seeQTL
rs11850979	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs11850979	ZFYVE21	cis	lymphoblastoid	seeQTL
rs11850979	KLC1	cis	parietal	SCAN
rs11850979	ZFYVE21	Cis_1M	lymphoblastoid	RTeQTL
rs11850979	CAMK2G	trans	parietal	SCAN
rs11850979	ZFYVE21	cis	multi-tissue	Pritchard
rs11850979	ZFYVE21	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104094400-104096800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104094400-104096800	Active TSS	Fetal Brain Female	brain
3	chr14:104094400-104097200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:104094400-104097200	Active TSS	Psoas Muscle	Psoas
5	chr14:104094400-104097400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr14:104094400-104097600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr14:104094600-104096600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr14:104094600-104096600	Active TSS	Gastric	stomach
9	chr14:104094600-104096600	Active TSS	Left Ventricle	heart
10	chr14:104094600-104096800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr14:104094600-104096800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr14:104094600-104096800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr14:104094600-104096800	Active TSS	Brain Substantia Nigra	brain
14	chr14:104094600-104096800	Active TSS	HepG2	liver
15	chr14:104094600-104097000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr14:104094600-104097200	Active TSS	Ovary	ovary
17	chr14:104094600-104097200	Active TSS	Right Atrium	heart
18	chr14:104094600-104097400	Active TSS	Aorta	Aorta
19	chr14:104094600-104097400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr14:104094800-104096600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:104094800-104096600	Active TSS	Esophagus	oesophagus
22	chr14:104094800-104096800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr14:104094800-104096800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:104094800-104096800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:104094800-104096800	Active TSS	Brain Anterior Caudate	brain
26	chr14:104094800-104096800	Active TSS	Brain Hippocampus Middle	brain
27	chr14:104094800-104096800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr14:104094800-104096800	Active TSS	GM12878-XiMat	blood
29	chr14:104094800-104097000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr14:104094800-104097000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr14:104094800-104097200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:104094800-104097400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:104095000-104096600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:104095000-104096600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:104095000-104096600	Active TSS	Brain Angular Gyrus	brain
36	chr14:104095000-104096600	Active TSS	Fetal Lung	lung
37	chr14:104095000-104096600	Active TSS	Lung	lung
38	chr14:104095000-104096600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr14:104095000-104096600	Active TSS	Spleen	Spleen
40	chr14:104095000-104096600	Active TSS	Hela-S3	cervix
41	chr14:104095000-104096800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr14:104095000-104096800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr14:104095000-104096800	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr14:104095000-104096800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:104095000-104096800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:104095000-104096800	Active TSS	Brain Cingulate Gyrus	brain
47	chr14:104095000-104096800	Active TSS	Colon Smooth Muscle	Colon
48	chr14:104095000-104096800	Active TSS	Fetal Intestine Large	intestine
49	chr14:104095000-104096800	Active TSS	Fetal Intestine Small	intestine
50	chr14:104095000-104096800	Active TSS	Fetal Stomach	stomach

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