Variant report

Variant	rs7875404
Chromosome Location	chr9:19087154-19087155
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	chr9:19086054..19088942-chr9:19092129..19094506,2	K562	blood:
2	chr9:19077380..19080397-chr9:19085594..19088171,3	K562	blood:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10113939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117076	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10120860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124438	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12002212	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341699	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12349511	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1932450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62563590	0.93[ASN][1000 genomes]
rs62563640	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475278	1.00[JPT][hapmap]
rs6475289	1.00[CHB][hapmap]
rs7024953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7025416	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7033648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7038785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7041472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7043607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7467294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7855439	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7860085	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7864679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7866883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7869183	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869414	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7875404	ADFP	cis	multi-tissue	Pritchard

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	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:19056600-19094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:19056600-19095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:19056600-19095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
19	chr9:19066400-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
21	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
22	chr9:19068800-19096800	Strong transcription	Fetal Thymus	thymus
23	chr9:19070000-19089400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:19070400-19090600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:19071200-19101200	Weak transcription	Psoas Muscle	Psoas
26	chr9:19073400-19087200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:19073600-19098400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:19074400-19094200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:19074400-19094600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:19075000-19089000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:19075400-19091200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:19075600-19087200	Weak transcription	K562	blood
33	chr9:19075600-19092000	Weak transcription	Fetal Kidney	kidney
34	chr9:19075800-19087800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:19077200-19091000	Weak transcription	Pancreas	Pancrea
36	chr9:19077400-19089000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:19077400-19089200	Weak transcription	HSMMtube	muscle
38	chr9:19077400-19089400	Weak transcription	Esophagus	oesophagus
39	chr9:19077400-19090600	Weak transcription	Brain Substantia Nigra	brain
40	chr9:19077400-19102200	Weak transcription	Gastric	stomach
41	chr9:19078000-19089400	Weak transcription	Right Ventricle	heart
42	chr9:19078000-19091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:19078200-19087200	Weak transcription	Brain Angular Gyrus	brain
44	chr9:19078200-19089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:19078200-19089200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:19078200-19091800	Weak transcription	Spleen	Spleen
47	chr9:19078600-19089200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:19078800-19089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:19079200-19092400	Strong transcription	A549	lung
50	chr9:19079200-19099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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