Variant report

Variant	rs10123378
Chromosome Location	chr9:96375217-96375218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96353488..96355423-chr9:96374627..96377387,2	K562	blood:
2	chr9:96374097..96376355-chr9:96382214..96384351,2	K562	blood:
3	chr9:96336833..96339118-chr9:96375167..96379434,3	MCF-7	breast:
4	chr9:96338137..96340211-chr9:96373633..96375791,2	K562	blood:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10114002	0.82[CHD][hapmap]
rs10116422	0.82[CHD][hapmap]
rs10117225	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10117691	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10156602	0.95[CHB][hapmap]
rs10739951	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10761238	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10761239	0.85[CHB][hapmap]
rs10761240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10761241	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10761242	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10821160	0.81[CEU][hapmap]
rs10821163	0.82[CEU][hapmap]
rs10821164	0.85[CHB][hapmap]
rs10821166	0.85[CHB][hapmap]
rs10821168	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.83[ASN][1000 genomes]
rs10821169	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821173	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821174	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821175	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821176	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821179	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10821180	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10821181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992792	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10992797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10992798	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10992799	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992800	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992805	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992860	0.86[MEX][hapmap]
rs1132004	0.90[MEX][hapmap]
rs12238738	0.90[MEX][hapmap]
rs13291079	0.92[CEU][hapmap]
rs13294381	0.83[ASN][1000 genomes]
rs1412048	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1412049	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2001610	0.86[MEX][hapmap]
rs2398845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2398846	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2398847	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2895249	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750359	0.90[MEX][hapmap]
rs4568663	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7040340	0.82[MEX][hapmap]
rs7857266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3408240	chr9:96375131-96379629	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10123378	HIATL1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96352400-96384600	Weak transcription	NHLF	lung
2	chr9:96361400-96380400	Weak transcription	Fetal Brain Male	brain
3	chr9:96361600-96379400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:96363200-96392000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:96363600-96383600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:96364200-96380600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:96366400-96379400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:96366600-96386600	Weak transcription	Fetal Heart	heart
9	chr9:96372800-96376000	Weak transcription	Right Ventricle	heart
10	chr9:96372800-96392000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:96373000-96377200	Enhancers	Psoas Muscle	Psoas
12	chr9:96373000-96379400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:96373200-96376000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr9:96373400-96377000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:96373400-96379400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:96373400-96379400	Weak transcription	Brain Anterior Caudate	brain
17	chr9:96373400-96379400	Weak transcription	Fetal Intestine Large	intestine
18	chr9:96373400-96386200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:96373400-96387000	Weak transcription	Fetal Brain Female	brain
20	chr9:96373400-96390000	Weak transcription	Primary B cells from cord blood	blood
21	chr9:96373600-96379400	Weak transcription	Brain Germinal Matrix	brain
22	chr9:96373800-96379000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:96374000-96375400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr9:96374200-96375600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr9:96374200-96376400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:96374200-96376600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr9:96374400-96375400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr9:96374400-96375400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:96374400-96375600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr9:96374400-96375600	Enhancers	Duodenum Mucosa	Duodenum
31	chr9:96374400-96375600	Enhancers	HUVEC	blood vessel
32	chr9:96374400-96375800	Enhancers	HMEC	breast
33	chr9:96374400-96376000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:96374400-96376400	Enhancers	GM12878-XiMat	blood
35	chr9:96374400-96376600	Enhancers	Colon Smooth Muscle	Colon
36	chr9:96374400-96376800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:96374400-96377000	Enhancers	Primary B cells from peripheral blood	blood
38	chr9:96374600-96375400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:96374600-96375400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr9:96374600-96375600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr9:96374600-96375600	Enhancers	Esophagus	oesophagus
42	chr9:96374600-96375600	Enhancers	Rectal Smooth Muscle	rectum
43	chr9:96374600-96375800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:96374600-96375800	Enhancers	Ovary	ovary
45	chr9:96374600-96375800	Strong transcription	Dnd41	blood
46	chr9:96374600-96375800	Enhancers	NHEK	skin
47	chr9:96374600-96376000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr9:96374600-96376600	Enhancers	Left Ventricle	heart
49	chr9:96374600-96377000	Weak transcription	Fetal Kidney	kidney
50	chr9:96374600-96378000	Enhancers	Spleen	Spleen

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