Variant report

Variant	rs7037787
Chromosome Location	chr9:19051563-19051564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19050026..19052622-chr9:19058219..19060617,2	K562	blood:
2	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10122990	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10123400	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10123520	0.80[ASN][1000 genomes]
rs10123624	0.85[ASN][1000 genomes]
rs10125646	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125677	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1048169	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757024	0.85[ASN][1000 genomes]
rs10757025	0.85[ASN][1000 genomes]
rs10811103	0.81[ASN][1000 genomes]
rs10811104	0.85[ASN][1000 genomes]
rs10811107	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10811108	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10963921	0.84[ASN][1000 genomes]
rs10963924	0.86[ASN][1000 genomes]
rs10963925	0.85[ASN][1000 genomes]
rs10963942	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1154672	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154673	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12236347	0.82[ASN][1000 genomes]
rs12343169	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12380322	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13287117	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13287517	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1932457	0.82[ASN][1000 genomes]
rs2130570	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2130571	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2233798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35133951	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4392990	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394488	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439216	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977278	0.85[ASN][1000 genomes]
rs4977490	0.86[AMR][1000 genomes]
rs4977492	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62563593	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62563594	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6475311	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6475312	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475313	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475314	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6475315	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs68092871	0.84[ASN][1000 genomes]
rs7022450	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022807	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7026281	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7027346	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7035738	0.84[ASN][1000 genomes]
rs7036118	0.84[ASN][1000 genomes]
rs7036182	0.84[ASN][1000 genomes]
rs7036301	0.84[ASN][1000 genomes]
rs7037772	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7043115	0.85[ASN][1000 genomes]
rs7043507	0.85[ASN][1000 genomes]
rs7045844	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7467618	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850487	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7854974	0.85[ASN][1000 genomes]
rs7855250	0.84[ASN][1000 genomes]
rs7856768	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9298795	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7037787	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:19048800-19051800	Active TSS	HMEC	breast
6	chr9:19048800-19052000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:19048800-19052000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:19049000-19052000	Active TSS	Osteobl	bone
9	chr9:19049800-19052000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr9:19050000-19052000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr9:19050000-19052000	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr9:19050200-19051600	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr9:19050200-19051800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr9:19050200-19051800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
15	chr9:19050200-19052000	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr9:19050200-19052000	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr9:19050400-19051600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:19050400-19051600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:19050400-19051600	Flanking Active TSS	Fetal Brain Male	brain
20	chr9:19050400-19051600	Transcr. at gene 5' and 3'	HSMM	muscle
21	chr9:19050400-19051800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:19050400-19051800	Transcr. at gene 5' and 3'	Fetal Lung	lung
23	chr9:19050400-19052000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:19050600-19051600	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr9:19050600-19051600	Enhancers	Esophagus	oesophagus
26	chr9:19050600-19051600	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr9:19050600-19051600	Enhancers	Spleen	Spleen
28	chr9:19050600-19051800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:19050600-19051800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr9:19050600-19052000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:19050600-19052000	Flanking Active TSS	Dnd41	blood
32	chr9:19050600-19052800	Flanking Active TSS	Fetal Brain Female	brain
33	chr9:19050600-19056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:19050800-19051800	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:19050800-19051800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr9:19050800-19051800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr9:19050800-19051800	Flanking Active TSS	Thymus	Thymus
42	chr9:19050800-19052000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:19050800-19052000	Enhancers	Stomach Mucosa	stomach
44	chr9:19050800-19052200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr9:19050800-19052400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:19050800-19052600	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
47	chr9:19050800-19052600	Enhancers	Small Intestine	intestine
48	chr9:19050800-19074200	Weak transcription	Lung	lung
49	chr9:19051000-19051600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr9:19051000-19051600	Genic enhancers	Primary B cells from peripheral blood	blood

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