Variant report

Variant	rs1036788
Chromosome Location	chr4:77201487-77201488
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	chr4:77068994..77070621-chr4:77200458..77203318,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1036787	0.90[AFR][1000 genomes]
rs11097320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441911	0.92[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530295	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530296	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1530297	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1530298	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1969148	0.84[ASN][1000 genomes]
rs1969149	0.84[ASN][1000 genomes]
rs28592037	0.88[AFR][1000 genomes]
rs2869872	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532316	0.85[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs768981	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461559	chr4:77192838-77204500	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594695	chr4:77192838-77204500	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1036788	CCNI	cis	lymphoblastoid	seeQTL
rs1036788	FAM47E	cis	cerebellum	SCAN
rs1036788	NAAA	cis	parietal	SCAN
rs1036788	FAM47E	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173600-77202000	Weak transcription	Psoas Muscle	Psoas
2	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:77180000-77202000	Weak transcription	Gastric	stomach
4	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
5	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
6	chr4:77187600-77202000	Weak transcription	Brain Substantia Nigra	brain
7	chr4:77188000-77202200	Weak transcription	Brain Angular Gyrus	brain
8	chr4:77188200-77202000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:77193000-77201800	Weak transcription	Left Ventricle	heart
11	chr4:77193000-77202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:77193000-77202200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:77198200-77201600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:77199600-77201800	Weak transcription	Small Intestine	intestine
17	chr4:77199800-77203600	Enhancers	Liver	Liver
18	chr4:77199800-77204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:77200000-77201600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:77200200-77201600	Weak transcription	Fetal Intestine Small	intestine
21	chr4:77200400-77201800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:77200800-77202800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:77200800-77203000	Enhancers	Stomach Mucosa	stomach
24	chr4:77201200-77202400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:77201400-77201600	Enhancers	A549	lung
26	chr4:77201400-77202400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:77201400-77202400	Enhancers	Placenta	Placenta
28	chr4:77201400-77202400	Enhancers	Pancreas	Pancrea
29	chr4:77201400-77202400	Enhancers	Right Atrium	heart
30	chr4:77201400-77203000	Enhancers	Adipose Nuclei	Adipose
31	chr4:77201400-77203000	Enhancers	Duodenum Mucosa	Duodenum
32	chr4:77201400-77203000	Enhancers	HepG2	liver
33	chr4:77201400-77203600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr4:77201400-77204400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:77201400-77205800	Enhancers	Fetal Intestine Large	intestine

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