Variant report

Variant	rs414829
Chromosome Location	chr5:9552525-9552526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:9552447..9554138-chr5:9558237..9561822,3	MCF-7	breast:
2	chr5:9540715..9542331-chr5:9550727..9553558,2	MCF-7	breast:
3	chr5:9545641..9548478-chr5:9550713..9552547,2	K562	blood:
4	chr5:9546514..9548478-chr5:9550572..9552547,2	K562	blood:

Variant related genes	Relation type
ENSG00000250786	Chromatin interaction
ENSG00000112902	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10462868	0.96[ASN][1000 genomes]
rs11749803	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398337	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1508798	0.93[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]
rs1614229	0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1651283	1.00[JPT][hapmap]
rs1651284	1.00[JPT][hapmap]
rs1651285	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1651286	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1706987	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1706992	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17263917	0.94[CEU][hapmap]
rs17328863	0.88[CEU][hapmap]
rs17328904	0.88[CEU][hapmap]
rs268555	0.85[ASN][1000 genomes]
rs268556	0.85[ASN][1000 genomes]
rs374218	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777371	0.93[YRI][hapmap]
rs3798089	0.93[YRI][hapmap]
rs3798099	0.85[ASN][1000 genomes]
rs414396	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs422309	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs431288	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432989	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs456885	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs460234	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461337	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs461750	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs464621	0.85[ASN][1000 genomes]
rs4702633	0.93[YRI][hapmap]
rs56344213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60322708	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605126	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881628	0.93[YRI][hapmap]
rs6882326	0.93[YRI][hapmap]
rs73051829	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases
20	nsv881586	chr5:9549386-9578794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs414829	CTD-2001E22.2	cis	Artery Aorta	GTEx
rs414829	CTD-2001E22.2	cis	Adipose Subcutaneous	GTEx
rs414829	CTD-2001E22.2	cis	Esophagus Mucosa	GTEx
rs414829	CTD-2001E22.2	cis	Nerve Tibial	GTEx
rs414829	CTD-2001E22.2	cis	Muscle Skeletal	GTEx
rs414829	CTD-2001E22.2	cis	Stomach	GTEx
rs414829	CTD-2001E22.2	cis	lung	GTEx
rs414829	CTD-2001E22.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9547000-9554200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:9548200-9552800	Weak transcription	Stomach Mucosa	stomach
3	chr5:9548200-9553000	Weak transcription	Fetal Kidney	kidney
4	chr5:9548200-9554000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:9548200-9554200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:9548200-9556200	Weak transcription	Right Ventricle	heart
7	chr5:9548200-9558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:9548200-9558400	Weak transcription	Liver	Liver
9	chr5:9548400-9553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:9548400-9558400	Weak transcription	Fetal Heart	heart
11	chr5:9548600-9552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:9548600-9558400	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:9548800-9552800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:9549000-9552600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:9549000-9552600	Strong transcription	Fetal Intestine Large	intestine
16	chr5:9549000-9552600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr5:9549000-9552800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:9549000-9553200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:9549000-9553200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr5:9549000-9553600	Strong transcription	Fetal Stomach	stomach
21	chr5:9549000-9553800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:9549000-9553800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:9549000-9554000	Strong transcription	Fetal Muscle Leg	muscle
24	chr5:9549200-9552800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:9549200-9552800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:9549200-9552800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:9549200-9553000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:9549200-9553000	Strong transcription	Fetal Lung	lung
29	chr5:9549200-9553200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:9549200-9553200	Strong transcription	NH-A	brain
31	chr5:9549400-9553000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:9549400-9553800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:9549600-9552800	Strong transcription	Fetal Intestine Small	intestine
34	chr5:9550000-9553600	Strong transcription	NHDF-Ad	bronchial
35	chr5:9550200-9553000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:9550200-9554400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:9550200-9558400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:9550200-9563000	Weak transcription	Brain Substantia Nigra	brain
39	chr5:9550400-9552800	Strong transcription	Osteobl	bone
40	chr5:9550400-9553600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:9550400-9553800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:9550400-9554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:9550600-9553600	Weak transcription	Left Ventricle	heart
44	chr5:9550600-9558400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:9550800-9557400	Weak transcription	NHEK	skin
46	chr5:9551000-9552800	Strong transcription	Ovary	ovary
47	chr5:9551000-9553000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr5:9551200-9553400	Weak transcription	Lung	lung
49	chr5:9551200-9554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:9551200-9557400	Weak transcription	Muscle Satellite Cultured Cells	--

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