Variant report

Variant	rs4977490
Chromosome Location	chr9:19054387-19054388
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	chr9:19049135..19050932-chr9:19052465..19054640,2	K562	blood:
2	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10122990	0.85[AMR][1000 genomes]
rs10123400	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes]
rs10123520	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs10123624	0.86[CHB][hapmap]
rs10125646	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1048169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10757024	0.84[JPT][hapmap]
rs10811110	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10963924	0.84[JPT][hapmap]
rs10963925	0.81[JPT][hapmap]
rs10963942	0.83[CEU][hapmap]
rs11515236	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs1154672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs1154673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes]
rs12236347	0.86[CHB][hapmap]
rs13287117	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13287517	0.86[AMR][1000 genomes]
rs1932457	0.86[CHB][hapmap]
rs2233798	0.81[AMR][1000 genomes]
rs35133951	0.81[AMR][1000 genomes]
rs4392990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4394488	0.85[AMR][1000 genomes]
rs4977492	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6475311	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6475313	0.81[AMR][1000 genomes]
rs6475314	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6475315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7022576	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7027346	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7037772	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7037787	0.86[AMR][1000 genomes]
rs7045844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs7467137	0.84[JPT][hapmap]
rs7467618	0.83[CEU][hapmap];0.96[YRI][hapmap]
rs7854858	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs7856768	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7859259	0.93[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4977490	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	chr9:19050600-19056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:19050800-19074200	Weak transcription	Lung	lung
7	chr9:19051000-19056600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:19051000-19059000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:19051200-19057000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:19051400-19054400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:19051400-19054800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:19051400-19055400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:19051400-19056600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:19051400-19056600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:19051400-19056600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:19051400-19056600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:19051400-19056600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
19	chr9:19051600-19055200	Weak transcription	Placenta	Placenta
20	chr9:19051600-19055600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:19051600-19055800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:19051600-19056400	Weak transcription	Fetal Intestine Small	intestine
23	chr9:19051600-19056400	Weak transcription	Hela-S3	cervix
24	chr9:19051600-19056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:19051600-19056600	Weak transcription	Esophagus	oesophagus
26	chr9:19051600-19056600	Weak transcription	Fetal Intestine Large	intestine
27	chr9:19051600-19056600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:19051600-19056600	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:19051600-19056600	Weak transcription	Fetal Thymus	thymus
30	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
31	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:19051800-19055800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:19051800-19056000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:19051800-19056000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr9:19051800-19056200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:19051800-19056600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:19051800-19056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:19051800-19056600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:19051800-19056800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:19051800-19057000	Weak transcription	A549	lung
41	chr9:19051800-19057200	Weak transcription	Brain Substantia Nigra	brain
42	chr9:19051800-19057400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:19051800-19059000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:19051800-19059400	Weak transcription	HSMMtube	muscle
45	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
46	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:19052000-19055800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:19052000-19056200	Weak transcription	Osteobl	bone
49	chr9:19052000-19056600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:19052000-19056600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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