Variant report

Variant	rs7856768
Chromosome Location	chr9:19056754-19056755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19049339..19052176-chr9:19056143..19057826,3	MCF-7	breast:
2	chr9:19054696..19057530-chr9:19066725..19069005,3	MCF-7	breast:
3	chr9:19048116..19054448-chr9:19056568..19061765,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10122990	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123400	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123520	0.81[ASN][1000 genomes]
rs10123624	0.86[ASN][1000 genomes]
rs10125646	0.91[ASN][1000 genomes]
rs10125677	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1048169	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757024	0.86[ASN][1000 genomes]
rs10757025	0.86[ASN][1000 genomes]
rs10811103	0.82[ASN][1000 genomes]
rs10811104	0.86[ASN][1000 genomes]
rs10811107	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10811108	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10811110	0.82[ASN][1000 genomes]
rs10963921	0.85[ASN][1000 genomes]
rs10963924	0.87[ASN][1000 genomes]
rs10963925	0.86[ASN][1000 genomes]
rs10963942	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1154672	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1154673	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12164262	0.82[ASN][1000 genomes]
rs12236347	0.83[ASN][1000 genomes]
rs12343169	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12380322	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13287117	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13287517	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1932457	0.83[ASN][1000 genomes]
rs2130570	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2130571	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2233798	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35133951	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4392990	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4394488	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4439216	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4977278	0.86[ASN][1000 genomes]
rs4977490	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4977492	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62563593	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62563594	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475311	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6475312	0.86[ASN][1000 genomes]
rs6475313	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475314	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6475315	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs68092871	0.85[ASN][1000 genomes]
rs7022450	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022807	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7026281	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7027346	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7035738	0.85[ASN][1000 genomes]
rs7036118	0.85[ASN][1000 genomes]
rs7036182	0.85[ASN][1000 genomes]
rs7036301	0.85[ASN][1000 genomes]
rs7037772	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7037787	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7043115	0.86[ASN][1000 genomes]
rs7043507	0.86[ASN][1000 genomes]
rs7045844	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7467618	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7850487	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7854858	0.82[ASN][1000 genomes]
rs7854974	0.86[ASN][1000 genomes]
rs7855250	0.85[ASN][1000 genomes]
rs7855338	0.82[ASN][1000 genomes]
rs7859259	0.85[ASN][1000 genomes]
rs9298795	0.87[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	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
5	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
6	esv3408862	chr9:19056310-19058050	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7856768	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:19050800-19074200	Weak transcription	Lung	lung
6	chr9:19051000-19059000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:19051200-19057000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
9	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
10	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:19051800-19056800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:19051800-19057000	Weak transcription	A549	lung
13	chr9:19051800-19057200	Weak transcription	Brain Substantia Nigra	brain
14	chr9:19051800-19057400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:19051800-19059000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:19051800-19059400	Weak transcription	HSMMtube	muscle
17	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
18	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:19052000-19056800	Weak transcription	Primary T cells from cord blood	blood
20	chr9:19052000-19056800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:19052000-19056800	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:19052000-19056800	Weak transcription	NH-A	brain
23	chr9:19052000-19057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:19052000-19057000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:19052000-19057200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:19052000-19057200	Weak transcription	HMEC	breast
27	chr9:19052000-19057800	Weak transcription	NHLF	lung
28	chr9:19052000-19059000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:19052000-19061800	Weak transcription	Stomach Mucosa	stomach
30	chr9:19052000-19062600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
32	chr9:19052200-19056800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:19052200-19056800	Weak transcription	GM12878-XiMat	blood
34	chr9:19052200-19057000	Weak transcription	Thymus	Thymus
35	chr9:19052200-19057200	Weak transcription	Psoas Muscle	Psoas
36	chr9:19052400-19056800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:19052400-19056800	Weak transcription	K562	blood
38	chr9:19052400-19057200	Weak transcription	Primary B cells from cord blood	blood
39	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
40	chr9:19052600-19056800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:19052600-19057000	Weak transcription	HSMM	muscle
42	chr9:19052600-19057200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr9:19052600-19057800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:19052600-19059200	Weak transcription	Brain Anterior Caudate	brain
45	chr9:19052600-19065000	Weak transcription	Small Intestine	intestine
46	chr9:19052800-19056800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:19052800-19057000	Weak transcription	Fetal Heart	heart
48	chr9:19052800-19057200	Weak transcription	Adipose Nuclei	Adipose
49	chr9:19052800-19059200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:19052800-19059200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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