Variant report

Variant	rs678778
Chromosome Location	chr15:42446208-42446209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42444865..42447535-chr15:42448992..42450632,2	K562	blood:
2	chr15:42445910..42447999-chr15:42452272..42454986,2	K562	blood:
3	chr15:42444314..42447262-chr15:42447408..42450681,4	K562	blood:
4	chr15:42440587..42442217-chr15:42443778..42446321,2	K562	blood:
5	chr15:42429960..42432547-chr15:42445427..42447652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction
ENSG00000168907	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10220859	0.84[EUR][1000 genomes]
rs10775126	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs10851409	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs11070370	0.81[CHB][hapmap]
rs11631983	0.82[CHB][hapmap]
rs12438509	1.00[CEU][hapmap]
rs12440087	1.00[CEU][hapmap]
rs1619030	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1624183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1659212	0.82[CHB][hapmap]
rs1659213	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1659218	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1659219	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1659222	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1678985	0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1678986	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1678992	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1678993	0.91[CHB][hapmap]
rs1679002	0.81[ASN][1000 genomes]
rs1679009	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs1679010	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1679012	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs16972770	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16972776	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16972887	1.00[CEU][hapmap]
rs16973008	1.00[CEU][hapmap]
rs16973045	1.00[CEU][hapmap]
rs16973060	1.00[CEU][hapmap]
rs1703750	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs1703754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703755	0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1712418	0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs2289295	0.82[CHB][hapmap]
rs2620386	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2918459	0.82[CHB][hapmap]
rs2918460	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs2918461	0.81[CHB][hapmap]
rs3743005	1.00[CEU][hapmap]
rs3743006	0.81[CHB][hapmap]
rs3743007	1.00[CEU][hapmap]
rs3743008	1.00[CEU][hapmap]
rs3825785	1.00[CEU][hapmap]
rs4506867	1.00[CEU][hapmap]
rs4923932	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4923940	0.82[CHB][hapmap]
rs4923945	1.00[CEU][hapmap]
rs4924627	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924630	1.00[CEU][hapmap]
rs4924645	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs4924653	0.82[CHB][hapmap]
rs4924658	0.82[CHB][hapmap]
rs4924672	1.00[CEU][hapmap]
rs4924673	1.00[CEU][hapmap]
rs598360	0.81[ASN][1000 genomes]
rs60486546	0.90[EUR][1000 genomes]
rs60506946	0.93[EUR][1000 genomes]
rs622442	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs622714	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624841	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633934	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6493027	0.82[CHB][hapmap]
rs660126	0.92[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs677878	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs681029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7180279	1.00[CEU][hapmap]
rs7181742	0.81[CHB][hapmap]
rs7183015	0.82[CHB][hapmap]
rs7183546	0.81[CHB][hapmap]
rs73403545	0.93[EUR][1000 genomes]
rs73403546	0.93[EUR][1000 genomes]
rs73403548	0.93[EUR][1000 genomes]
rs73403550	0.87[EUR][1000 genomes]
rs74009020	0.93[EUR][1000 genomes]
rs8024732	0.81[CHB][hapmap]
rs8031315	0.81[CHB][hapmap]
rs8033080	0.90[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs8036187	0.92[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs8036596	0.81[CHB][hapmap]
rs8037020	0.81[CHB][hapmap]
rs9920921	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv3361173	chr15:42445160-42449558	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3446241	chr15:42445660-42448658	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42436000-42452000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42439400-42451200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42439400-42451800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:42439600-42448600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:42441200-42450600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:42441800-42451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:42442600-42447000	Enhancers	Esophagus	oesophagus
8	chr15:42442600-42447400	Weak transcription	Spleen	Spleen
9	chr15:42443400-42447600	Enhancers	Gastric	stomach
10	chr15:42443600-42447000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr15:42443600-42447600	Enhancers	Colonic Mucosa	Colon
12	chr15:42443800-42446400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr15:42443800-42448000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr15:42444000-42451600	Weak transcription	HUVEC	blood vessel
15	chr15:42444400-42446400	Strong transcription	Fetal Intestine Small	intestine
16	chr15:42444400-42446600	Weak transcription	Fetal Thymus	thymus
17	chr15:42444400-42447000	Weak transcription	Fetal Kidney	kidney
18	chr15:42444400-42450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:42444600-42448200	Weak transcription	HSMMtube	muscle
20	chr15:42444600-42450200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:42444800-42446600	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:42444800-42447000	Weak transcription	Fetal Lung	lung
23	chr15:42444800-42449800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:42444800-42450200	Weak transcription	Brain Substantia Nigra	brain
25	chr15:42444800-42450200	Weak transcription	HSMM	muscle
26	chr15:42444800-42450600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:42444800-42450600	Weak transcription	Brain Germinal Matrix	brain
28	chr15:42444800-42451000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:42444800-42451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:42444800-42451200	Weak transcription	Aorta	Aorta
31	chr15:42445000-42446400	Weak transcription	HMEC	breast
32	chr15:42445000-42446600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:42445000-42446600	Weak transcription	Fetal Heart	heart
34	chr15:42445000-42446600	Weak transcription	NHEK	skin
35	chr15:42445000-42449800	Weak transcription	Brain Anterior Caudate	brain
36	chr15:42445000-42450000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:42445000-42450000	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:42445000-42450200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:42445000-42451400	Weak transcription	Brain Angular Gyrus	brain
40	chr15:42445200-42446600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:42445400-42447000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:42445400-42451000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:42445400-42451000	Weak transcription	Right Atrium	heart
44	chr15:42445600-42446600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:42445600-42449000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:42445800-42446400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:42445800-42447000	Weak transcription	Lung	lung
48	chr15:42445800-42450200	Weak transcription	Psoas Muscle	Psoas
49	chr15:42446000-42450000	Enhancers	Right Ventricle	heart
50	chr15:42446000-42451000	Weak transcription	H9 Cell Line	embryonic stem cell

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