Variant report

Variant	rs1790740
Chromosome Location	chr11:67130122-67130123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67070995..67072990-chr11:67129655..67131719,2	K562	blood:
2	chr11:67042036..67043663-chr11:67129940..67132127,2	K562	blood:
3	chr11:67119765..67126816-chr11:67129168..67134805,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAD9A-3	chr11:67129885-67130179	NONHSAT022410

Variant related genes	Relation type
ENSG00000172830	Chromatin interaction
ENSG00000175482	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10896167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896168	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10896169	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11227756	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs11227788	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11601700	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11608094	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12276833	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12288107	0.92[ASW][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs12290164	0.92[ASW][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs12788752	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1540135	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1558256	0.92[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1626067	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs1638566	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638567	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1638571	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1638574	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1638586	0.92[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1790733	0.92[ASW][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1790747	0.92[ASW][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs2066496	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2071007	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2256154	0.95[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2286620	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap]
rs2429460	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2429462	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2514256	0.92[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2514258	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34596169	0.83[ASN][1000 genomes]
rs3758943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3781941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781943	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3927807	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap]
rs4024520	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4255546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4542419	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4930192	1.00[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs4930197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930418	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56337023	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs660960	0.92[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs674499	0.92[ASW][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7106352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480390	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs872109	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs872110	0.92[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
5	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv468603	chr11:67033076-67164495	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv555253	chr11:67033076-67164495	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
9	nsv1047890	chr11:67058231-67184436	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
11	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67121600-67132600	Weak transcription	Fetal Brain Female	brain
2	chr11:67121800-67132800	Weak transcription	Fetal Brain Male	brain
3	chr11:67123400-67131800	Weak transcription	Aorta	Aorta
4	chr11:67125000-67130400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:67125000-67131400	Weak transcription	Lung	lung
6	chr11:67125000-67131800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:67125000-67132000	Weak transcription	Esophagus	oesophagus
8	chr11:67125000-67132000	Weak transcription	Left Ventricle	heart
9	chr11:67125000-67132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:67125000-67132200	Weak transcription	Gastric	stomach
11	chr11:67125000-67132200	Weak transcription	Ovary	ovary
12	chr11:67125000-67132200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:67125000-67132400	Weak transcription	Pancreas	Pancrea
14	chr11:67125000-67133400	Weak transcription	Fetal Kidney	kidney
15	chr11:67125000-67137600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:67125200-67131800	Weak transcription	Right Ventricle	heart
17	chr11:67125200-67132000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:67125200-67132200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:67125200-67133600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:67125200-67138200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:67125200-67139200	Weak transcription	Small Intestine	intestine
22	chr11:67125600-67131800	Weak transcription	Adipose Nuclei	Adipose
23	chr11:67125600-67133600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:67125600-67136600	Weak transcription	HUVEC	blood vessel
25	chr11:67125800-67131400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:67125800-67131600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:67125800-67131800	Weak transcription	Fetal Intestine Large	intestine
28	chr11:67125800-67132200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:67125800-67133600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:67125800-67133800	Weak transcription	K562	blood
31	chr11:67126000-67131400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:67126000-67131400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:67126000-67131400	Weak transcription	Spleen	Spleen
34	chr11:67126000-67131800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:67126000-67131800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:67126000-67132000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:67126000-67132000	Weak transcription	NHEK	skin
38	chr11:67126000-67132200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:67126000-67132200	Weak transcription	NHDF-Ad	bronchial
40	chr11:67126000-67133400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:67126000-67133600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:67126000-67133800	Weak transcription	HSMMtube	muscle
43	chr11:67126200-67130200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:67126200-67131200	Weak transcription	NHLF	lung
45	chr11:67126200-67131400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:67126200-67131400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:67126200-67131400	Weak transcription	HMEC	breast
48	chr11:67126200-67131600	Weak transcription	Hela-S3	cervix
49	chr11:67126200-67131800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:67126200-67131800	Weak transcription	NH-A	brain

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