Variant report

Variant	rs706017
Chromosome Location	chr7:27139878-27139879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:27135386-27149832	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:27139372-27143752	MCF10A-Er-Src	breast:	n/a	n/a
3	CHD1	chr7:27134717-27152399	IMR90	lung:	n/a	chr7:27141647-27141657

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:27137201-27143270..7:27162022-27164727	H1-hESC	embryonic stem cell:	embryo

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EVX1-13	chr7:27139238-27139884	ENSG00000233429.5
2	lnc-EVX1-13	chr7:27139238-27139884	ENSG00000233429.5

Variant related genes	Relation type
HOXA1	TF binding region
ENSG00000253552	Chromatin interaction
HOXA1	LncRNA region
HOXA4	LncRNA region

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2522827	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522828	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706018	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
7	nsv887857	chr7:27120689-27229549	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv824039	chr7:27121825-27294951	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
9	nsv824040	chr7:27121870-27295010	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
10	nsv887858	chr7:27127231-27188659	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
11	nsv887860	chr7:27127231-27196069	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv887859	chr7:27127231-27196113	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
13	nsv887861	chr7:27127231-27206688	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
14	nsv887862	chr7:27127231-27217359	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
15	nsv887863	chr7:27127231-27243106	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
16	nsv887864	chr7:27127231-27243962	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
17	nsv887865	chr7:27127231-27247279	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
18	nsv887866	chr7:27127231-27248373	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
19	nsv887867	chr7:27127231-27252246	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
20	nsv824041	chr7:27128039-27294951	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
21	nsv606463	chr7:27135314-27182245	Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
22	nsv887868	chr7:27135314-27202289	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
23	nsv887869	chr7:27135314-27297791	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
24	nsv887870	chr7:27136308-27154737	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
25	nsv887871	chr7:27136308-27179814	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
26	nsv887872	chr7:27136308-27181437	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
27	nsv887873	chr7:27136308-27186495	Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
28	nsv887874	chr7:27136308-27196069	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
29	nsv606464	chr7:27138478-27168590	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs706017	HOTAIRM1	cis	Skin Sun Exposed Lower leg	GTEx
rs706017	HOTAIRM1	cis	Esophagus Muscularis	GTEx
rs706017	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs706017	HOTAIRM1	cis	Whole Blood	GTEx
rs706017	HOTAIRM1	cis	Artery Tibial	GTEx
rs706017	HOTAIRM1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27134800-27140200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr7:27137000-27146800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:27137400-27140600	Weak transcription	HSMMtube	muscle
4	chr7:27137400-27140800	Transcr. at gene 5' and 3'	NHEK	skin
5	chr7:27137600-27149000	Weak transcription	HepG2	liver
6	chr7:27138000-27144200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:27138000-27144800	Weak transcription	A549	lung
8	chr7:27138200-27141600	Weak transcription	Spleen	Spleen
9	chr7:27138400-27140400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:27138600-27141000	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr7:27138600-27141400	Strong transcription	HSMM	muscle
12	chr7:27138600-27143000	Active TSS	Stomach Smooth Muscle	stomach
13	chr7:27138800-27141200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr7:27138800-27143400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:27139000-27140200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr7:27139000-27140400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:27139000-27140400	Weak transcription	Esophagus	oesophagus
18	chr7:27139000-27140400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:27139000-27140400	Weak transcription	Lung	lung
20	chr7:27139000-27140400	Weak transcription	Psoas Muscle	Psoas
21	chr7:27139000-27141400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:27139200-27140000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:27139200-27140200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:27139200-27140200	Weak transcription	Aorta	Aorta
25	chr7:27139200-27140200	Weak transcription	Colonic Mucosa	Colon
26	chr7:27139200-27140200	Weak transcription	Right Atrium	heart
27	chr7:27139200-27140400	Enhancers	Adipose Nuclei	Adipose
28	chr7:27139200-27140400	Enhancers	Colon Smooth Muscle	Colon
29	chr7:27139200-27140400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr7:27139200-27140400	Enhancers	Fetal Intestine Large	intestine
31	chr7:27139200-27140400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr7:27139200-27140400	Enhancers	Rectal Smooth Muscle	rectum
33	chr7:27139200-27140400	Enhancers	Stomach Mucosa	stomach
34	chr7:27139200-27140800	Transcr. at gene 5' and 3'	HMEC	breast
35	chr7:27139200-27141600	Strong transcription	Osteobl	bone
36	chr7:27139400-27140000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:27139400-27140000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:27139400-27140200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr7:27139400-27140400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:27139400-27141400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:27139600-27140200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr7:27139600-27140400	Bivalent Enhancer	Fetal Kidney	kidney
43	chr7:27139600-27140800	Weak transcription	NHDF-Ad	bronchial
44	chr7:27139600-27143200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:27139800-27140000	Bivalent Enhancer	Fetal Lung	lung
46	chr7:27139800-27140000	Active TSS	NHLF	lung
47	chr7:27139800-27140200	Active TSS	Fetal Stomach	stomach
48	chr7:27139800-27140200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
49	chr7:27139800-27141000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:27139800-27141400	Active TSS	Duodenum Smooth Muscle	Duodenum

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