Variant report

Variant	rs3861678
Chromosome Location	chr14:104322026-104322027
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104321265..104323478-chr14:104393162..104395402,2	MCF-7	breast:
2	chr14:104309239..104311339-chr14:104321164..104323172,2	MCF-7	breast:
3	chr14:104321174..104323261-chr14:104360889..104363923,3	MCF-7	breast:
4	chr14:104321542..104325039-chr14:104354434..104358481,6	MCF-7	breast:
5	chr14:104319613..104324063-chr14:104346589..104349290,5	MCF-7	breast:
6	chr14:104321201..104322886-chr14:104337478..104339238,2	MCF-7	breast:
7	chr14:104290311..104292684-chr14:104319761..104322144,2	MCF-7	breast:
8	chr14:104321815..104323849-chr14:104376770..104378345,2	MCF-7	breast:
9	chr14:104321544..104323309-chr14:104582015..104584779,2	MCF-7	breast:
10	chr14:104320527..104323273-chr14:104369468..104371736,3	MCF-7	breast:
11	chr14:104320605..104323611-chr14:104373502..104376733,3	MCF-7	breast:
12	chr14:104320208..104324271-chr14:104346660..104350133,4	MCF-7	breast:
13	chr14:104284106..104288227-chr14:104321092..104325164,4	MCF-7	breast:
14	chr14:104321329..104324090-chr14:104325687..104328665,2	K562	blood:
15	chr14:104320014..104324951-chr14:104331915..104336985,8	MCF-7	breast:
16	chr14:104320594..104323018-chr14:104349310..104351645,2	MCF-7	breast:
17	chr14:104319048..104323751-chr14:104384975..104388146,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000156414	Chromatin interaction
ENSG00000207568	Chromatin interaction
ENSG00000156411	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10129899	0.95[ASN][1000 genomes]
rs1040813	0.83[JPT][hapmap]
rs11160759	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11160760	0.82[JPT][hapmap]
rs11160762	0.82[JPT][hapmap]
rs1155751	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs11623546	0.82[JPT][hapmap]
rs11624184	0.82[JPT][hapmap]
rs11625740	0.89[CHB][hapmap]
rs11626377	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11628332	0.82[JPT][hapmap]
rs11847468	0.82[JPT][hapmap]
rs1187416	0.83[JPT][hapmap]
rs1187417	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588797	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879501	0.82[JPT][hapmap]
rs12879529	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12880821	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12883337	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12885018	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12885509	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12886637	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12888002	0.82[EUR][1000 genomes]
rs12889993	0.82[JPT][hapmap]
rs12890354	0.82[EUR][1000 genomes]
rs12890430	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890822	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12890837	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12891175	0.82[JPT][hapmap]
rs12891477	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12892186	0.81[ASN][1000 genomes]
rs12892189	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893623	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475007	0.82[JPT][hapmap]
rs1535097	0.82[JPT][hapmap]
rs1535098	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs17791722	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997913	0.82[JPT][hapmap]
rs2223937	0.82[JPT][hapmap]
rs2295141	0.82[JPT][hapmap]
rs2368560	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2887282	0.82[JPT][hapmap]
rs34596177	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35085624	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35740217	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818085	0.82[JPT][hapmap]
rs4900594	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4900597	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4900600	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs4906363	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4906364	0.81[AMR][1000 genomes]
rs4906365	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4906376	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906377	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906378	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4906379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6575997	0.82[JPT][hapmap]
rs6576006	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6576008	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66676135	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66953418	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7142769	0.81[EUR][1000 genomes]
rs7156834	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7159810	0.82[JPT][hapmap]
rs722637	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs8003653	0.82[JPT][hapmap]
rs8004408	0.82[JPT][hapmap]
rs8005225	0.82[JPT][hapmap]
rs8005594	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs8016014	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs8017200	0.85[EUR][1000 genomes]
rs8548	0.92[CEU][hapmap];0.94[CHB][hapmap]
rs876002	0.82[JPT][hapmap]
rs9888591	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
3	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
4	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
5	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
6	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
7	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
9	esv1838047	chr14:104283104-104359121	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	esv1818596	chr14:104312697-104359121	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	esv1836134	chr14:104312697-104359121	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	esv1837236	chr14:104313426-104332759	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv566028	chr14:104314023-104332759	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3861678	RP11-73M18.8	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104315200-104327600	Weak transcription	Ovary	ovary
2	chr14:104319800-104323400	Enhancers	Placenta	Placenta
3	chr14:104320000-104322600	Flanking Active TSS	HepG2	liver
4	chr14:104320000-104325400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr14:104320200-104323200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:104320200-104323600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr14:104320200-104325200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:104320400-104322600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:104320400-104322800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:104320400-104323000	Enhancers	Fetal Lung	lung
11	chr14:104320400-104323000	Enhancers	Lung	lung
12	chr14:104320400-104323200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr14:104320400-104323600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr14:104320400-104323800	Enhancers	Spleen	Spleen
15	chr14:104320600-104323400	Enhancers	Fetal Muscle Trunk	muscle
16	chr14:104320600-104323400	Enhancers	HUVEC	blood vessel
17	chr14:104320600-104323800	Enhancers	Fetal Muscle Leg	muscle
18	chr14:104320800-104323400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr14:104321000-104322400	Enhancers	Adipose Nuclei	Adipose
20	chr14:104321000-104322800	Enhancers	Duodenum Mucosa	Duodenum
21	chr14:104321000-104322800	Enhancers	Gastric	stomach
22	chr14:104321000-104323000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:104321000-104323000	Enhancers	Esophagus	oesophagus
24	chr14:104321000-104323600	Enhancers	Pancreas	Pancrea
25	chr14:104321200-104322400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr14:104321200-104322800	Enhancers	Fetal Intestine Large	intestine
27	chr14:104321200-104322800	Enhancers	NHEK	skin
28	chr14:104321200-104323000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:104321200-104323000	Enhancers	Fetal Thymus	thymus
30	chr14:104321200-104323000	Enhancers	Stomach Mucosa	stomach
31	chr14:104321200-104323200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:104321200-104323600	Enhancers	Fetal Intestine Small	intestine
33	chr14:104321400-104322200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr14:104321400-104322200	Enhancers	Brain Germinal Matrix	brain
35	chr14:104321400-104322200	Enhancers	Brain Hippocampus Middle	brain
36	chr14:104321400-104322400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:104321400-104322600	Enhancers	Fetal Heart	heart
38	chr14:104321400-104322800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:104321400-104322800	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr14:104321400-104322800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr14:104321400-104323000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr14:104321400-104323400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr14:104321400-104323600	Enhancers	Fetal Stomach	stomach
44	chr14:104321600-104322800	Enhancers	HMEC	breast
45	chr14:104321600-104323200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr14:104321600-104323600	Enhancers	Left Ventricle	heart
47	chr14:104321800-104322200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr14:104321800-104322600	Weak transcription	Right Ventricle	heart
49	chr14:104321800-104322800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr14:104321800-104323600	Enhancers	HUES48 Cell Line	embryonic stem cell

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