Variant report

Variant	rs242088
Chromosome Location	chr22:33219887-33219888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32920308-32927723..22:33219668-33224847	K562	blood:
2	chr22:33219487..33221924-chr22:33222975..33225306,3	K562	blood:

Variant related genes	Relation type
ENSG00000185666	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13057881	0.81[CHB][hapmap]
rs2016293	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267180	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242071	0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs242072	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs242075	0.88[ASN][1000 genomes]
rs242076	0.87[JPT][hapmap]
rs242077	0.87[JPT][hapmap]
rs242078	0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.87[ASN][1000 genomes]
rs242082	0.83[ASN][1000 genomes]
rs242085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242089	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713996	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs737089	0.87[CHB][hapmap]
rs738992	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9609632	0.81[CHB][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs242088	SLC5A4	cis	parietal	SCAN
rs242088	GAL3ST1	cis	parietal	SCAN
rs242088	SLC5A4	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33201000-33227400	Weak transcription	Aorta	Aorta
2	chr22:33201200-33222800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:33201600-33226200	Weak transcription	NH-A	brain
4	chr22:33202000-33220000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr22:33203200-33223600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr22:33204600-33220200	Weak transcription	Brain Hippocampus Middle	brain
7	chr22:33204800-33227800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr22:33206400-33220800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:33206800-33224600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr22:33207000-33226200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:33211000-33221400	Genic enhancers	Adipose Nuclei	Adipose
12	chr22:33211000-33225600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr22:33211000-33225800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr22:33211000-33240400	Genic enhancers	Left Ventricle	heart
15	chr22:33211400-33220600	Weak transcription	Fetal Kidney	kidney
16	chr22:33212400-33220800	Weak transcription	Fetal Intestine Large	intestine
17	chr22:33212600-33222600	Weak transcription	HSMMtube	muscle
18	chr22:33212600-33227000	Weak transcription	Liver	Liver
19	chr22:33213600-33227000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr22:33214400-33220800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr22:33214800-33222600	Weak transcription	Fetal Lung	lung
22	chr22:33215200-33222800	Enhancers	Fetal Heart	heart
23	chr22:33215200-33225800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:33215400-33220800	Weak transcription	Fetal Intestine Small	intestine
25	chr22:33215400-33222800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:33215400-33225600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:33215600-33222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:33216000-33226800	Weak transcription	Fetal Thymus	thymus
29	chr22:33216400-33220000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:33216400-33225600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr22:33216800-33220200	Weak transcription	Brain Anterior Caudate	brain
32	chr22:33216800-33223600	Weak transcription	Fetal Brain Male	brain
33	chr22:33217200-33222800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr22:33217400-33221200	Enhancers	Stomach Smooth Muscle	stomach
35	chr22:33217400-33222600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr22:33217400-33226400	Weak transcription	Ovary	ovary
37	chr22:33217600-33220600	Weak transcription	Colon Smooth Muscle	Colon
38	chr22:33217600-33221200	Enhancers	Right Atrium	heart
39	chr22:33217600-33222600	Weak transcription	NHEK	skin
40	chr22:33217800-33222200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr22:33217800-33226000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:33217800-33229000	Weak transcription	NHLF	lung
43	chr22:33217800-33248600	Weak transcription	Gastric	stomach
44	chr22:33218200-33220200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr22:33218200-33220200	Strong transcription	HSMM	muscle
46	chr22:33218400-33222600	Weak transcription	HepG2	liver
47	chr22:33218600-33220000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr22:33218600-33220600	Weak transcription	HMEC	breast
49	chr22:33218600-33221200	Enhancers	Right Ventricle	heart
50	chr22:33218600-33222600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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