Variant report

Variant	rs1004654
Chromosome Location	chr5:95203134-95203135
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95201904..95203629-chr5:95296910..95298882,2	K562	blood:
2	chr5:95197433..95200134-chr5:95202863..95204651,3	K562	blood:
3	chr5:95201531..95203525-chr5:95206404..95208684,2	K562	blood:

Variant related genes	Relation type
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction
ENSG00000250362	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10476660	0.82[TSI][hapmap]
rs12515492	1.00[CHD][hapmap]
rs12659828	0.88[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1465446	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[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873611	0.82[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1004654	CHD1	cis	parietal	SCAN
rs1004654	SPATA9	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:95195000-95208400	Weak transcription	Ovary	ovary
4	chr5:95195200-95217400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:95195600-95206200	Weak transcription	Brain Anterior Caudate	brain
6	chr5:95197200-95203200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr5:95197800-95204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:95198600-95206200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:95199000-95204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:95199000-95204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:95199200-95206000	Weak transcription	Fetal Heart	heart
12	chr5:95199400-95203200	Enhancers	Osteobl	bone
13	chr5:95199400-95203400	Weak transcription	Fetal Thymus	thymus
14	chr5:95199400-95204000	Weak transcription	Primary T cells from cord blood	blood
15	chr5:95199400-95204000	Weak transcription	Dnd41	blood
16	chr5:95199400-95204400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:95199400-95204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:95199400-95205000	Weak transcription	HUVEC	blood vessel
19	chr5:95199400-95205200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:95199400-95210000	Weak transcription	Right Ventricle	heart
21	chr5:95199600-95204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:95200000-95203200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:95200000-95206000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:95200000-95206200	Weak transcription	Esophagus	oesophagus
25	chr5:95200000-95206200	Weak transcription	Psoas Muscle	Psoas
26	chr5:95200400-95205200	Weak transcription	Adipose Nuclei	Adipose
27	chr5:95200800-95205400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:95201000-95205400	Weak transcription	Liver	Liver
29	chr5:95201000-95205800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:95201200-95205200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:95201200-95205200	Weak transcription	Left Ventricle	heart
32	chr5:95201200-95205400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:95201200-95205800	Weak transcription	NHLF	lung
34	chr5:95201200-95206000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr5:95201200-95206000	Weak transcription	Colonic Mucosa	Colon
36	chr5:95201200-95206000	Weak transcription	Lung	lung
37	chr5:95201200-95206000	Weak transcription	Right Atrium	heart
38	chr5:95201200-95206000	Weak transcription	Small Intestine	intestine
39	chr5:95201400-95203200	Enhancers	HepG2	liver
40	chr5:95201400-95212200	Weak transcription	Placenta	Placenta
41	chr5:95201800-95203600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:95201800-95203800	Weak transcription	Brain Substantia Nigra	brain
43	chr5:95201800-95206000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:95201800-95206000	Weak transcription	Stomach Mucosa	stomach
45	chr5:95202000-95204000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr5:95202000-95206000	Weak transcription	Fetal Intestine Small	intestine
47	chr5:95202000-95206200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:95202000-95212600	Weak transcription	Gastric	stomach
49	chr5:95202200-95203200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:95202200-95203200	Enhancers	Primary monocytes fromperipheralblood	blood

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