Variant report

Variant	rs5752785
Chromosome Location	chr22:29146503-29146504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29137433..29139398-chr22:29143624..29147097,3	K562	blood:
2	chr22:29136760..29140497-chr22:29144206..29149800,9	MCF-7	breast:
3	chr22:29144367..29147213-chr22:29158314..29160831,2	MCF-7	breast:
4	chr22:29140753..29143117-chr22:29145529..29147123,2	K562	blood:
5	chr22:29145305..29148162-chr22:29185055..29187826,2	K562	blood:
6	chr22:29145130..29148116-chr22:29224104..29225824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1884816	0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs1884817	0.82[CHB][hapmap]
rs2017309	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236142	0.82[YRI][hapmap]
rs2347443	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4820792	0.82[AMR][1000 genomes]
rs5752777	0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs5752788	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762766	0.86[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6519761	0.82[YRI][hapmap]
rs714191	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289973	0.84[AMR][1000 genomes]
rs743185	0.84[GIH][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5752785	TFIP11	cis	cerebellum	SCAN
rs5752785	RGL4	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29139200-29153800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:29139400-29149400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr22:29139400-29156400	Weak transcription	Stomach Mucosa	stomach
4	chr22:29139600-29146800	Strong transcription	Primary T cells from cord blood	blood
5	chr22:29139600-29148200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr22:29139600-29148600	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr22:29139600-29149600	Weak transcription	K562	blood
8	chr22:29139800-29146600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr22:29139800-29146800	Strong transcription	Fetal Intestine Large	intestine
10	chr22:29139800-29147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:29139800-29147400	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr22:29139800-29147600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr22:29139800-29147800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr22:29139800-29147800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr22:29139800-29147800	Strong transcription	Lung	lung
16	chr22:29139800-29148200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr22:29139800-29148200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr22:29139800-29148400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:29139800-29149000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:29139800-29149000	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:29139800-29149200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr22:29139800-29149400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:29139800-29150600	Strong transcription	Fetal Stomach	stomach
24	chr22:29139800-29156000	Weak transcription	HMEC	breast
25	chr22:29140000-29147200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr22:29140000-29147600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr22:29140000-29148200	Strong transcription	Placenta	Placenta
28	chr22:29140000-29148600	Weak transcription	Fetal Heart	heart
29	chr22:29140000-29149200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:29140000-29150000	Strong transcription	Fetal Intestine Small	intestine
31	chr22:29140200-29147000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr22:29140800-29152000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr22:29140800-29155800	Weak transcription	Fetal Brain Female	brain
34	chr22:29141000-29153200	Weak transcription	Aorta	Aorta
35	chr22:29141200-29156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:29141400-29149800	Weak transcription	A549	lung
37	chr22:29141800-29147200	Weak transcription	Psoas Muscle	Psoas
38	chr22:29143000-29148000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:29143400-29148000	Strong transcription	NHEK	skin
40	chr22:29143400-29156600	Weak transcription	Brain Substantia Nigra	brain
41	chr22:29143600-29147400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:29143600-29154000	Weak transcription	Thymus	Thymus
43	chr22:29143600-29155600	Weak transcription	Gastric	stomach
44	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr22:29143800-29149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:29143800-29153600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr22:29143800-29155600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr22:29143800-29156000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr22:29143800-29156400	Weak transcription	Brain Angular Gyrus	brain
50	chr22:29144000-29147600	Strong transcription	Liver	Liver

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