Variant report

Variant	rs171211
Chromosome Location	chr5:68495083-68495084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68487593..68492001-chr5:68493438..68496143,4	K562	blood:
2	chr5:68483247..68487010-chr5:68493814..68496489,4	K562	blood:
3	chr5:68483247..68486892-chr5:68492488..68496489,4	K562	blood:
4	chr17:73772377..73774350-chr5:68494079..68495837,2	K562	blood:

Variant related genes	Relation type
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10045526	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10063757	0.99[ASN][1000 genomes]
rs10063969	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12513817	0.87[ASN][1000 genomes]
rs13362324	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs164709	0.97[ASN][1000 genomes]
rs164789	0.97[ASN][1000 genomes]
rs2242350	0.99[ASN][1000 genomes]
rs28768211	0.94[ASN][1000 genomes]
rs34893396	0.99[ASN][1000 genomes]
rs350104	0.96[ASN][1000 genomes]
rs350106	0.97[ASN][1000 genomes]
rs35308484	0.99[ASN][1000 genomes]
rs3890705	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs426392	0.97[ASN][1000 genomes]
rs4266362	0.80[AMR][1000 genomes]
rs62373181	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6450026	0.91[ASN][1000 genomes]
rs6450027	0.90[ASN][1000 genomes]
rs676012	0.99[ASN][1000 genomes]
rs6866993	0.80[AMR][1000 genomes]

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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs171211	TAF9	cis	Esophagus Muscularis	GTEx
rs171211	CCDC125	cis	lung	GTEx
rs171211	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs171211	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
3	chr5:68486000-68505800	Weak transcription	Ovary	ovary
4	chr5:68486000-68513600	Weak transcription	Gastric	stomach
5	chr5:68486200-68496200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:68486200-68496200	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:68486200-68497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:68486200-68497600	Weak transcription	Fetal Heart	heart
9	chr5:68486200-68497600	Weak transcription	Pancreas	Pancrea
10	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
15	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
16	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
18	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:68486200-68509400	Weak transcription	HSMM	muscle
22	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:68486400-68496400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:68486400-68496800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:68486400-68502400	Weak transcription	NH-A	brain
26	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
27	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
28	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
29	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
31	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
32	chr5:68486400-68513000	Weak transcription	Osteobl	bone
33	chr5:68486600-68497200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:68486600-68502600	Weak transcription	NHLF	lung
35	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
36	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:68487600-68495400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:68487600-68498000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:68487600-68500400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:68487600-68500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:68487600-68500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:68487600-68503000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr5:68487600-68503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:68487800-68495800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:68488200-68501600	Strong transcription	Dnd41	blood

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