Variant report

Variant	rs9291126
Chromosome Location	chr4:6968942-6968943
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6953603..6955195-chr4:6967201..6969667,2	K562	blood:
2	chr4:6964966..6966973-chr4:6967560..6969658,4	MCF-7	breast:
3	chr4:6962320..6964054-chr4:6967764..6970067,3	K562	blood:
4	chr4:6968058..6971311-chr4:6972075..6975359,5	K562	blood:
5	chr4:6918816..6920459-chr4:6968873..6971872,2	MCF-7	breast:
6	chr4:6966970..6969558-chr4:6972075..6974539,2	K562	blood:

Variant related genes	Relation type
ENSG00000265953	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10012590	0.83[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10025310	0.84[CEU][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11732898	0.85[CHD][hapmap]
rs11934364	1.00[CHB][hapmap]
rs11938701	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11944897	0.86[ASN][1000 genomes]
rs12503027	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12510715	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs13107989	0.86[ASN][1000 genomes]
rs13108082	0.87[ASN][1000 genomes]
rs13111887	0.87[ASN][1000 genomes]
rs13122119	0.80[ASN][1000 genomes]
rs13148395	0.86[ASN][1000 genomes]
rs13149411	0.80[ASN][1000 genomes]
rs2301817	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301818	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2301819	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.80[ASN][1000 genomes]
rs3188939	0.83[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs34221933	0.86[ASN][1000 genomes]
rs34335938	0.80[ASN][1000 genomes]
rs34463709	0.80[ASN][1000 genomes]
rs34481892	0.80[ASN][1000 genomes]
rs34959511	0.80[ASN][1000 genomes]
rs35170004	0.80[ASN][1000 genomes]
rs3892490	0.85[CHD][hapmap]
rs3894945	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4234788	0.87[ASN][1000 genomes]
rs4234791	0.80[ASN][1000 genomes]
rs4234793	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4327487	0.85[YRI][hapmap]
rs4376137	0.86[YRI][hapmap]
rs4423873	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs4428285	1.00[CHB][hapmap]
rs4544710	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4689059	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs4689563	0.80[ASN][1000 genomes]
rs4689564	0.80[ASN][1000 genomes]
rs4689565	0.80[ASN][1000 genomes]
rs4689566	0.81[ASN][1000 genomes]
rs4689567	0.81[ASN][1000 genomes]
rs4689568	0.85[CHD][hapmap]
rs4689575	0.82[CEU][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4689579	0.80[ASN][1000 genomes]
rs62289166	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446559	0.87[ASN][1000 genomes]
rs66530709	0.80[ASN][1000 genomes]
rs66640699	0.80[ASN][1000 genomes]
rs66931928	0.80[ASN][1000 genomes]
rs66992702	0.80[ASN][1000 genomes]
rs6811496	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816660	0.87[ASN][1000 genomes]
rs6818744	0.83[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6834102	0.86[ASN][1000 genomes]
rs6835187	0.93[YRI][hapmap]
rs6840780	0.86[ASN][1000 genomes]
rs6854776	0.83[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7655773	0.86[ASN][1000 genomes]
rs7661952	0.86[ASN][1000 genomes]
rs7673901	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7675524	0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs7685667	0.86[ASN][1000 genomes]
rs7689324	0.86[YRI][hapmap]
rs8180337	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9291126	OTOP1	cis	cerebellum	SCAN
rs9291126	HMX1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
2	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
3	chr4:6946600-6969000	Weak transcription	Dnd41	blood
4	chr4:6955800-6976000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:6956000-6976000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:6956400-6969200	Weak transcription	K562	blood
7	chr4:6957600-6970400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:6957600-6973800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:6957600-6976000	Weak transcription	Fetal Lung	lung
10	chr4:6957800-6976000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:6958400-6975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:6958800-6969400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:6962200-6969600	Weak transcription	Fetal Brain Female	brain
14	chr4:6964200-6969000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:6964200-6969600	Weak transcription	Esophagus	oesophagus
16	chr4:6964200-6976000	Weak transcription	Brain Germinal Matrix	brain
17	chr4:6964800-6969400	Weak transcription	Fetal Stomach	stomach
18	chr4:6964800-6969600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:6964800-6973400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:6965000-6969000	Weak transcription	Fetal Thymus	thymus
21	chr4:6965000-6976000	Weak transcription	A549	lung
22	chr4:6965200-6969200	Weak transcription	Colonic Mucosa	Colon
23	chr4:6965200-6969600	Weak transcription	Right Atrium	heart
24	chr4:6965200-6970400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:6965200-6971600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:6965200-6973400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:6965200-6976000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:6965200-6976000	Weak transcription	Stomach Mucosa	stomach
29	chr4:6965200-6976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:6965400-6969200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:6965400-6969200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:6965400-6969200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:6965400-6969200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:6965400-6969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:6965400-6969400	Weak transcription	Brain Anterior Caudate	brain
36	chr4:6965400-6969600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:6965400-6969600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr4:6965400-6969600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:6965400-6969600	Weak transcription	Left Ventricle	heart
40	chr4:6965400-6969600	Weak transcription	Lung	lung
41	chr4:6965400-6969600	Weak transcription	Right Ventricle	heart
42	chr4:6965400-6969600	Weak transcription	HUVEC	blood vessel
43	chr4:6965400-6969800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:6965400-6970000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:6965400-6973000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:6965400-6973000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:6965400-6973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:6965400-6973400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:6965400-6973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:6965400-6973600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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