Variant report

Variant	rs11563327
Chromosome Location	chr7:27071888-27071889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27071114..27072708-chr7:27126763..27129361,2	K562	blood:
2	7:27071265-27080138..7:27181770-27195105	K562	blood:

Variant related genes	Relation type
ENSG00000272801	Chromatin interaction
ENSG00000106004	Chromatin interaction
ENSG00000254369	Chromatin interaction
ENSG00000105997	Chromatin interaction
ENSG00000273433	Chromatin interaction
ENSG00000106006	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10227231	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10227553	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10238645	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10242572	0.90[JPT][hapmap]
rs10242754	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10256250	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10270187	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10272190	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10272457	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10486483	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10486485	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12530718	1.00[AFR][1000 genomes]
rs12534899	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12534901	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12534912	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12535784	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12540388	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs17323934	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17377696	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17436410	0.87[AMR][1000 genomes]
rs17471061	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17471088	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2030136	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2031811	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2079138	0.90[EUR][1000 genomes]
rs2248744	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2254463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2264802	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2264803	0.83[ASN][1000 genomes]
rs2391362	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2428416	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2428417	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2428418	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2428421	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2428425	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2428431	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2462900	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2462904	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2462906	0.87[EUR][1000 genomes]
rs2462908	0.90[EUR][1000 genomes]
rs2462910	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2465264	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465270	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2465271	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465274	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2522824	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2522825	0.88[EUR][1000 genomes]
rs2522826	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2648076	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2693659	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2693662	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2693665	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2693668	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2712234	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2712238	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2712242	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2712244	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2712245	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2712246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712248	0.89[EUR][1000 genomes]
rs2712250	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3801803	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs3801805	0.90[JPT][hapmap]
rs3801807	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801808	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801810	0.90[JPT][hapmap]
rs3801812	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801813	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801814	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801815	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801816	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs55889667	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56144845	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6461979	0.90[JPT][hapmap]
rs7791513	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7804356	0.89[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv967485	chr7:27066773-27082518	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11563327	HOXA2	cis	Whole Blood	GTEx
rs11563327	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27070200-27072000	Enhancers	Hela-S3	cervix
2	chr7:27070200-27072200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr7:27070200-27072800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr7:27070200-27072800	Enhancers	NHEK	skin
5	chr7:27070200-27073000	Enhancers	HSMMtube	muscle
6	chr7:27070400-27072800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr7:27070600-27072000	Enhancers	Stomach Mucosa	stomach
8	chr7:27070800-27072600	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:27071000-27072000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:27071000-27072000	Enhancers	Rectal Smooth Muscle	rectum
11	chr7:27071000-27072200	Enhancers	Primary T cells from cord blood	blood
12	chr7:27071000-27072200	Enhancers	Dnd41	blood
13	chr7:27071000-27072200	Enhancers	HUVEC	blood vessel
14	chr7:27071000-27072600	Enhancers	Fetal Heart	heart
15	chr7:27071000-27072800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:27071000-27072800	Enhancers	Fetal Kidney	kidney
17	chr7:27071000-27073200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:27071200-27072000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:27071200-27072000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr7:27071200-27072000	Enhancers	Colon Smooth Muscle	Colon
21	chr7:27071200-27072200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:27071200-27072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr7:27071200-27073000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:27071200-27073000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr7:27071200-27073200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:27071400-27072000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:27071400-27072000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:27071400-27072000	Enhancers	HSMM	muscle
29	chr7:27071400-27072800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:27071400-27073000	Enhancers	HMEC	breast
31	chr7:27071600-27072000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr7:27071600-27072200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr7:27071600-27072200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr7:27071600-27072200	Enhancers	Osteobl	bone
35	chr7:27071600-27072400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:27071600-27072600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr7:27071600-27072800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr7:27071600-27072800	Enhancers	NHLF	lung
39	chr7:27071800-27072000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:27071800-27072000	Enhancers	GM12878-XiMat	blood
41	chr7:27071800-27072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:27071800-27072200	Enhancers	Primary B cells from cord blood	blood
43	chr7:27071800-27072200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr7:27071800-27072400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:27071800-27072800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:27071800-27072800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:27071800-27072800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:27071800-27072800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:27071800-27072800	Enhancers	NHDF-Ad	bronchial
50	chr7:27071800-27073000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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