Variant report

Variant	rs7022613
Chromosome Location	chr9:19051208-19051209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19050026..19052622-chr9:19058219..19060617,2	K562	blood:
2	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:
3	chr9:19049276..19051385-chr9:19371232..19373694,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction
ENSG00000272842	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10119019	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10757023	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs10811094	0.82[MKK][hapmap]
rs10811098	0.82[MKK][hapmap]
rs10963922	0.81[ASW][hapmap];0.81[CEU][hapmap];0.92[LWK][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs10963932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963935	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963936	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963938	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10963939	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10963948	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10963949	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10963956	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13286328	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13302748	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2095545	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2171953	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28753724	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3824369	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7022093	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7026929	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7031375	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038917	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72696466	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7859319	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7022613	FAM29A	Cis_1M	lymphoblastoid	RTeQTL
rs7022613	FAM29A	cis	normal skin	skin_eQTL
rs7022613	RRAGA	cis	cerebellum	SCAN
rs7022613	PLIN2	cis	lymphoblastoid	seeQTL
rs7022613	IFNB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048400-19051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr9:19048600-19051400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:19048800-19051800	Active TSS	HMEC	breast
8	chr9:19048800-19052000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:19048800-19052000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:19049000-19051400	Active TSS	Pancreas	Pancrea
11	chr9:19049000-19052000	Active TSS	Osteobl	bone
12	chr9:19049600-19051400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:19049800-19051400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr9:19049800-19051400	Flanking Active TSS	HUVEC	blood vessel
15	chr9:19049800-19052000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr9:19050000-19051400	Flanking Active TSS	Liver	Liver
17	chr9:19050000-19052000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr9:19050000-19052000	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr9:19050200-19051400	Flanking Active TSS	Hela-S3	cervix
20	chr9:19050200-19051600	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr9:19050200-19051800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr9:19050200-19051800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
23	chr9:19050200-19052000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr9:19050200-19052000	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr9:19050400-19051400	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr9:19050400-19051600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:19050400-19051600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:19050400-19051600	Flanking Active TSS	Fetal Brain Male	brain
29	chr9:19050400-19051600	Transcr. at gene 5' and 3'	HSMM	muscle
30	chr9:19050400-19051800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:19050400-19051800	Transcr. at gene 5' and 3'	Fetal Lung	lung
32	chr9:19050400-19052000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:19050600-19051400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:19050600-19051400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr9:19050600-19051600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr9:19050600-19051600	Enhancers	Esophagus	oesophagus
37	chr9:19050600-19051600	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr9:19050600-19051600	Enhancers	Spleen	Spleen
39	chr9:19050600-19051800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:19050600-19051800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr9:19050600-19052000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:19050600-19052000	Flanking Active TSS	Dnd41	blood
43	chr9:19050600-19052800	Flanking Active TSS	Fetal Brain Female	brain
44	chr9:19050600-19056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:19050800-19051400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:19050800-19051400	Weak transcription	Gastric	stomach

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