Variant report

Variant	rs6479541
Chromosome Location	chr9:97203788-97203789
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	chr9:97202408..97204318-chr9:97206434..97208098,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10114295	0.88[EUR][1000 genomes]
rs10115864	0.87[ASN][1000 genomes]
rs10116979	0.88[EUR][1000 genomes]
rs10122398	0.92[ASN][1000 genomes]
rs10125631	0.88[EUR][1000 genomes]
rs10125744	0.92[ASN][1000 genomes]
rs10283669	0.87[ASN][1000 genomes]
rs10441776	0.88[EUR][1000 genomes]
rs1061835	0.87[ASN][1000 genomes]
rs10993191	0.90[ASN][1000 genomes]
rs10993194	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993201	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12338230	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12338572	0.92[ASN][1000 genomes]
rs12341403	0.87[ASN][1000 genomes]
rs12343123	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12343977	0.88[EUR][1000 genomes]
rs16911832	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1878875	0.87[ASN][1000 genomes]
rs2406663	0.87[EUR][1000 genomes]
rs28459299	0.88[EUR][1000 genomes]
rs28477240	0.88[EUR][1000 genomes]
rs28575335	0.88[EUR][1000 genomes]
rs28715696	0.88[EUR][1000 genomes]
rs28802403	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55936246	0.92[ASN][1000 genomes]
rs55962682	0.92[ASN][1000 genomes]
rs56404236	0.83[ASN][1000 genomes]
rs56413623	0.88[EUR][1000 genomes]
rs6479545	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479549	0.87[EUR][1000 genomes]
rs7022386	0.88[EUR][1000 genomes]
rs7024607	0.83[ASN][1000 genomes]
rs7025878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7027704	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7027860	0.88[EUR][1000 genomes]
rs7028388	0.88[EUR][1000 genomes]
rs7030326	0.87[ASN][1000 genomes]
rs7030967	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7034153	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7036474	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037298	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7040774	0.83[ASN][1000 genomes]
rs7041219	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7042219	0.88[EUR][1000 genomes]
rs7042434	0.80[EUR][1000 genomes]
rs7042468	0.88[EUR][1000 genomes]
rs7045712	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7046779	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73529936	0.90[EUR][1000 genomes]
rs7850084	0.85[EUR][1000 genomes]
rs7856786	0.87[ASN][1000 genomes]
rs7858126	0.87[EUR][1000 genomes]
rs7859955	0.87[ASN][1000 genomes]
rs7868600	0.88[EUR][1000 genomes]
rs7868703	0.88[EUR][1000 genomes]
rs7873527	0.89[EUR][1000 genomes]
rs9632920	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv33917	chr9:97185592-97216212	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6479541	HIATL1	cis	lung	GTEx
rs6479541	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs6479541	HIATL1	cis	Skin Sun Exposed Lower leg	GTEx
rs6479541	HIATL1	cis	Thyroid	GTEx
rs6479541	HIATL1	cis	Adipose Subcutaneous	GTEx
rs6479541	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs6479541	HIATL1	cis	Nerve Tibial	GTEx
rs6479541	HIATL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
2	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:97174200-97207000	Weak transcription	Lung	lung
6	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:97176000-97203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
9	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
10	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:97177400-97206400	Weak transcription	Gastric	stomach
12	chr9:97178000-97203800	Weak transcription	K562	blood
13	chr9:97178400-97206800	Weak transcription	Esophagus	oesophagus
14	chr9:97181000-97204800	Weak transcription	Placenta	Placenta
15	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:97181600-97206400	Weak transcription	HUVEC	blood vessel
18	chr9:97183000-97212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:97186200-97204200	Weak transcription	Spleen	Spleen
20	chr9:97187600-97205200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:97190400-97215800	Weak transcription	Ovary	ovary
22	chr9:97191600-97208200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:97192200-97210000	Weak transcription	NHDF-Ad	bronchial
24	chr9:97192200-97221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:97193000-97203800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:97193000-97211600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:97193800-97216000	Weak transcription	Brain Substantia Nigra	brain
28	chr9:97194000-97206600	Weak transcription	Right Ventricle	heart
29	chr9:97194000-97216000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:97194200-97208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:97194400-97211800	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:97195200-97211800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:97195200-97216000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:97195200-97216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:97195600-97213000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:97195600-97218000	Weak transcription	Pancreas	Pancrea
37	chr9:97197400-97203800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:97199400-97221400	Weak transcription	Psoas Muscle	Psoas
39	chr9:97199600-97209800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:97199600-97211600	Weak transcription	Fetal Kidney	kidney
41	chr9:97200000-97204200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:97200000-97211000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr9:97200800-97204600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:97201000-97205600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:97201000-97206200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:97201200-97206200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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