Variant report

Variant	rs12536138
Chromosome Location	chr7:7285869-7285870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIOS-5	chr7:7284225-7288212	NONHSAT119105

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10245376	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10263069	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10268210	0.83[ASN][1000 genomes]
rs1047763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11766771	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11767985	0.82[ASN][1000 genomes]
rs11767988	0.82[ASN][1000 genomes]
rs11772534	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772919	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468520	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2108784	0.87[ASN][1000 genomes]
rs2108787	0.84[ASN][1000 genomes]
rs2159191	0.87[ASN][1000 genomes]
rs4141099	0.86[CHB][hapmap]
rs5010184	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58096502	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58407878	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58529061	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6463661	0.84[ASN][1000 genomes]
rs6463662	0.84[ASN][1000 genomes]
rs6463663	0.84[ASN][1000 genomes]
rs6943933	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6944243	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7778301	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7811763	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
16	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription 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	33 gene(s)	inside rSNPs	diseases
17	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv464301	chr7:7252775-7442169	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv606035	chr7:7252775-7442169	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv469770	chr7:7261414-7453821	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
21	nsv433018	chr7:7269171-7348778	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
22	nsv606036	chr7:7273559-7343909	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
23	esv2756798	chr7:7280062-7441775	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12536138	C1GALT1	cis	Nerve Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7250800-7296600	Weak transcription	Spleen	Spleen
2	chr7:7256800-7297000	Weak transcription	Lung	lung
3	chr7:7257600-7298200	Weak transcription	Ovary	ovary
4	chr7:7257600-7299800	Weak transcription	Fetal Stomach	stomach
5	chr7:7260400-7297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:7261600-7296800	Weak transcription	Aorta	Aorta
7	chr7:7261600-7298000	Weak transcription	Pancreas	Pancrea
8	chr7:7261600-7299400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:7262200-7286600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:7265400-7287200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:7271400-7298200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:7271600-7287000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:7271800-7286000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:7271800-7289000	Weak transcription	Fetal Intestine Small	intestine
15	chr7:7272400-7295000	Weak transcription	Small Intestine	intestine
16	chr7:7272400-7296600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:7273000-7287000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:7273200-7291200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:7273400-7311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:7273600-7286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:7274600-7301600	Weak transcription	Brain Germinal Matrix	brain
22	chr7:7275000-7291200	Weak transcription	Hela-S3	cervix
23	chr7:7275400-7287200	Weak transcription	Stomach Mucosa	stomach
24	chr7:7275600-7298200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:7275600-7305400	Weak transcription	Gastric	stomach
26	chr7:7275800-7287000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr7:7276200-7298600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:7276800-7287400	Strong transcription	Dnd41	blood
29	chr7:7276800-7304000	Weak transcription	Fetal Brain Male	brain
30	chr7:7277200-7292800	Weak transcription	NHEK	skin
31	chr7:7277200-7306200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:7277600-7286000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:7277600-7296600	Weak transcription	Psoas Muscle	Psoas
34	chr7:7277600-7297800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:7277800-7294600	Weak transcription	Fetal Heart	heart
36	chr7:7278400-7299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:7278600-7286800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:7278800-7286000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:7279000-7287000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:7279000-7288600	Weak transcription	Brain Substantia Nigra	brain
41	chr7:7279000-7296600	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:7279000-7296800	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:7279200-7287200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:7279200-7298600	Weak transcription	Thymus	Thymus
45	chr7:7279200-7309800	Weak transcription	Brain Anterior Caudate	brain
46	chr7:7279800-7286800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:7279800-7296400	Weak transcription	HMEC	breast
48	chr7:7279800-7300000	Weak transcription	Fetal Brain Female	brain
49	chr7:7279800-7301000	Weak transcription	A549	lung
50	chr7:7279800-7304600	Weak transcription	NHDF-Ad	bronchial

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