Variant report

Variant	rs10963942
Chromosome Location	chr9:19080352-19080353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19078940..19081412-chr9:19100972..19102814,2	K562	blood:
2	chr9:19077380..19080397-chr9:19085594..19088171,3	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10122990	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10123400	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10123624	0.82[ASW][hapmap];0.88[CEU][hapmap]
rs10125646	0.88[CEU][hapmap]
rs1048169	0.94[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10757024	0.88[CEU][hapmap]
rs10811107	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10811108	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963921	0.88[CEU][hapmap]
rs10963924	0.88[CEU][hapmap]
rs10963925	0.91[CEU][hapmap]
rs1154672	0.94[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1154673	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12236347	0.88[CEU][hapmap]
rs12343169	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12380322	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13287117	0.80[AMR][1000 genomes]
rs13287517	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1932457	0.82[ASW][hapmap];0.88[CEU][hapmap]
rs2233798	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35133951	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4392990	0.94[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4394488	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4439216	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4977490	0.83[CEU][hapmap]
rs4977492	0.94[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.81[MKK][hapmap];0.87[YRI][hapmap]
rs62563593	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62563594	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475311	0.87[CEU][hapmap]
rs6475313	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6475314	0.82[AMR][1000 genomes]
rs6475315	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs7022450	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7022576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs7022807	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7026281	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7027346	0.94[ASW][hapmap]
rs7035738	0.87[CEU][hapmap]
rs7036118	0.88[CEU][hapmap]
rs7036182	0.87[CEU][hapmap]
rs7036301	0.88[CEU][hapmap]
rs7037772	0.83[AMR][1000 genomes]
rs7037787	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7045844	0.96[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7467618	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7850487	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7856768	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv2764156	chr9:19076894-19097008	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10963942	FAM29A	Cis_1M	lymphoblastoid	RTeQTL
rs10963942	RRAGA	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
4	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:19055800-19085200	Strong transcription	Liver	Liver
10	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:19056600-19094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:19056600-19095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:19056600-19095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:19056800-19083000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
23	chr9:19066400-19083400	Strong transcription	Placenta	Placenta
24	chr9:19066400-19085600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr9:19066400-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
27	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
28	chr9:19067000-19084800	Weak transcription	Colonic Mucosa	Colon
29	chr9:19067400-19086600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:19068800-19085400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:19068800-19096800	Strong transcription	Fetal Thymus	thymus
32	chr9:19069800-19080800	Strong transcription	Fetal Lung	lung
33	chr9:19070000-19089400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:19070400-19090600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:19071200-19101200	Weak transcription	Psoas Muscle	Psoas
36	chr9:19071400-19086800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:19072200-19083200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:19072400-19082800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:19073400-19082000	Strong transcription	Thymus	Thymus
40	chr9:19073400-19082600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:19073400-19087200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:19073600-19082800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:19073600-19098400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:19073800-19082400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr9:19074000-19083800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:19074000-19085200	Strong transcription	Fetal Stomach	stomach
47	chr9:19074400-19083200	Strong transcription	Adipose Nuclei	Adipose
48	chr9:19074400-19094200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:19074400-19094600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:19074600-19080800	Strong transcription	Rectal Mucosa Donor 29	rectum

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