Variant report

Variant	rs35039890
Chromosome Location	chr12:11281096-11281097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11271454..11274346-chr12:11279643..11282306,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11516172	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11522335	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13302964	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1451767	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs28542794	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34263586	0.81[EUR][1000 genomes]
rs34280471	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34315443	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34423519	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34490574	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34808476	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34825996	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34897085	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35034090	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35641223	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35760416	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35860793	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35962483	0.81[EUR][1000 genomes]
rs36057066	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3851591	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7135943	0.81[EUR][1000 genomes]
rs7296803	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7299875	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73051374	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7959172	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7970990	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7980237	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv1038709	chr12:11165117-11283834	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1804289	chr12:11166879-11294110	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv8917	chr12:11168232-11293747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv1835477	chr12:11174302-11298269	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv898782	chr12:11185236-11283763	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv3503785	chr12:11190186-11291382	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv3503796	chr12:11190186-11291382	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	esv3389516	chr12:11207203-11290088	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv6373	chr12:11209985-11282106	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	esv3350574	chr12:11212837-11284853	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
20	esv8675	chr12:11218264-11290113	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1042134	chr12:11220712-11328131	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv1043344	chr12:11220827-11308162	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	esv3350046	chr12:11256985-11292181	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv983285	chr12:11279606-11293601	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35039890	PRR4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11239200-11283600	Weak transcription	Fetal Thymus	thymus
2	chr12:11245200-11286000	Weak transcription	Ovary	ovary
3	chr12:11253000-11283200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:11260000-11297000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:11262200-11296400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:11262200-11296800	Weak transcription	Thymus	Thymus
7	chr12:11262200-11314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:11262800-11318200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:11265400-11297200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:11265800-11284000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:11266400-11296800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:11267200-11281600	Weak transcription	Fetal Stomach	stomach
13	chr12:11267800-11286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:11268200-11281800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:11268600-11283000	Weak transcription	Left Ventricle	heart
16	chr12:11268600-11312600	Weak transcription	Hela-S3	cervix
17	chr12:11270400-11286000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:11270400-11323200	Weak transcription	Fetal Kidney	kidney
19	chr12:11270600-11282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:11271000-11283000	Weak transcription	HSMMtube	muscle
21	chr12:11271200-11281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:11271200-11282400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:11271200-11285000	Weak transcription	Adipose Nuclei	Adipose
24	chr12:11271400-11281200	Weak transcription	Placenta	Placenta
25	chr12:11272400-11281800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:11272400-11286200	Weak transcription	NHEK	skin
27	chr12:11273400-11297200	Weak transcription	HUVEC	blood vessel
28	chr12:11273600-11281200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:11273800-11321800	Weak transcription	Osteobl	bone
30	chr12:11275000-11287200	Weak transcription	Fetal Brain Male	brain
31	chr12:11275800-11281200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:11276400-11281800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:11276400-11283200	Weak transcription	Aorta	Aorta
34	chr12:11276400-11295800	Weak transcription	Fetal Intestine Large	intestine
35	chr12:11276800-11292200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:11276800-11303600	Weak transcription	HSMM	muscle
37	chr12:11276800-11311800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:11277000-11281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:11277000-11281600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:11277000-11281600	Weak transcription	Fetal Lung	lung
41	chr12:11277000-11281800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:11277000-11286200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:11277000-11296000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:11277000-11297600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:11277400-11283200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:11277800-11281800	Weak transcription	Fetal Intestine Small	intestine
47	chr12:11278000-11281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:11278000-11294400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:11278200-11294400	Weak transcription	A549	lung
50	chr12:11278600-11297000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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