Variant report

Variant	rs4744345
Chromosome Location	chr9:97207669-97207670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97206178..97208805-chr9:97213845..97216691,2	K562	blood:
2	chr9:97202408..97204318-chr9:97206434..97208098,2	K562	blood:
3	chr9:97136576..97138289-chr9:97205602..97208468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148110	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10821345	0.97[ASN][1000 genomes]
rs10821352	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10993127	0.82[CHD][hapmap]
rs10993210	0.96[ASN][1000 genomes]
rs11789704	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12002028	0.94[ASN][1000 genomes]
rs12235970	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs12236219	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs12236578	0.94[ASN][1000 genomes]
rs16909983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16910109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1752784	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1752786	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2479615	0.81[TSI][hapmap]
rs2486632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2769813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2769816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2993948	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs4612412	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs55877910	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs594198	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60964095	0.81[ASN][1000 genomes]
rs61628907	0.94[ASN][1000 genomes]
rs639276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7042481	0.87[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs7848227	0.81[JPT][hapmap]
rs7858082	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9409544	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9409546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs9409547	0.81[TSI][hapmap]
rs9409550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409564	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409565	0.89[ASN][1000 genomes]
rs9409567	0.90[ASN][1000 genomes]
rs9409767	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409771	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409778	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409780	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409787	0.88[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4744345	HIATL1	cis	lymphoblastoid	seeQTL
rs4744345	ZNF484	cis	cerebellum	SCAN
rs4744345	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs4744345	HIATL1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
3	chr9:97177200-97209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:97181000-97208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:97183000-97212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:97190400-97215800	Weak transcription	Ovary	ovary
8	chr9:97191600-97208200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:97192200-97210000	Weak transcription	NHDF-Ad	bronchial
10	chr9:97192200-97221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:97193000-97211600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr9:97193800-97216000	Weak transcription	Brain Substantia Nigra	brain
13	chr9:97194000-97216000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:97194200-97208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:97194400-97211800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:97195200-97211800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:97195200-97216000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:97195200-97216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:97195600-97213000	Weak transcription	Fetal Intestine Small	intestine
20	chr9:97195600-97218000	Weak transcription	Pancreas	Pancrea
21	chr9:97199400-97221400	Weak transcription	Psoas Muscle	Psoas
22	chr9:97199600-97209800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:97199600-97211600	Weak transcription	Fetal Kidney	kidney
24	chr9:97200000-97211000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr9:97201400-97221400	Weak transcription	Stomach Mucosa	stomach
30	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr9:97201600-97209000	Weak transcription	Fetal Lung	lung
32	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:97202000-97211200	Weak transcription	NH-A	brain
34	chr9:97202000-97211800	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:97202000-97224200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr9:97202200-97215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:97202200-97216000	Weak transcription	Brain Angular Gyrus	brain
38	chr9:97202200-97225600	Strong transcription	Dnd41	blood
39	chr9:97202400-97222600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:97202800-97209800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:97202800-97211800	Weak transcription	Brain Germinal Matrix	brain
42	chr9:97203000-97215800	Weak transcription	Brain Anterior Caudate	brain
43	chr9:97203200-97214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:97203200-97225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:97203400-97211800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:97203600-97212400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr9:97203600-97212400	Strong transcription	Primary T cells from cord blood	blood
48	chr9:97203600-97212400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr9:97203600-97214000	Strong transcription	Primary B cells from cord blood	blood
50	chr9:97203800-97217000	Weak transcription	HepG2	liver

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