Variant report

Variant	rs9472236
Chromosome Location	chr6:44206750-44206751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44123357..44125146-chr6:44203946..44206894,2	K562	blood:
2	chr6:44138703..44140706-chr6:44205999..44208385,2	MCF-7	breast:
3	chr6:43737632..43739680-chr6:44205540..44207219,3	MCF-7	breast:
4	chr6:44139023..44142178-chr6:44202710..44207835,5	K562	blood:
5	chr6:44079762..44081284-chr6:44204790..44206941,2	K562	blood:
6	chr6:44199025..44201599-chr6:44203689..44206993,5	MCF-7	breast:
7	chr6:44202199..44204856-chr6:44206389..44207933,2	MCF-7	breast:
8	chr6:44094095..44096990-chr6:44204419..44207697,4	MCF-7	breast:
9	chr6:44093264..44095446-chr6:44204345..44207044,2	K562	blood:
10	chr6:44184911..44192138-chr6:44201380..44207306,8	MCF-7	breast:
11	chr6:44118511..44121325-chr6:44203702..44206845,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC29A1-2	chr6:44204713-44208319	NONHSAT112955

No data

Variant related genes	Relation type
ENSG00000272114	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000180992	Chromatin interaction
ENSG00000112759	Chromatin interaction
ENSG00000137216	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10948128	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11752427	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875324	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2039361	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282151	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3757283	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714772	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];1.00[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];0.99[ASN][1000 genomes]
rs476632	0.97[ASN][1000 genomes]
rs523891	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575034	0.88[ASN][1000 genomes]
rs9462978	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472238	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv885852	chr6:44185901-44222718	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' 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	90 gene(s)	inside rSNPs	diseases
4	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9472236	GPR115	cis	parietal	SCAN
rs9472236	SNORD73A	trans	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44204600-44207400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:44205800-44212800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44205800-44213200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:44206000-44206800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:44206000-44206800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:44206000-44206800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:44206000-44206800	Enhancers	Fetal Intestine Large	intestine
8	chr6:44206000-44206800	Enhancers	Fetal Intestine Small	intestine
9	chr6:44206000-44206800	Genic enhancers	Fetal Thymus	thymus
10	chr6:44206000-44207000	Enhancers	A549	lung
11	chr6:44206000-44207200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:44206000-44207400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:44206000-44207400	Enhancers	HMEC	breast
14	chr6:44206000-44212800	Weak transcription	Right Ventricle	heart
15	chr6:44206000-44213200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:44206000-44213400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:44206000-44213400	Weak transcription	Right Atrium	heart
18	chr6:44206200-44206800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:44206200-44206800	Enhancers	Brain Anterior Caudate	brain
20	chr6:44206200-44206800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:44206200-44206800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:44206200-44206800	Enhancers	K562	blood
23	chr6:44206200-44207200	Enhancers	HepG2	liver
24	chr6:44206200-44207400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:44206200-44207400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:44206200-44207400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:44206200-44207400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:44206200-44207400	Enhancers	NHEK	skin
29	chr6:44206200-44208400	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:44206200-44213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:44206200-44213200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:44206200-44213200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:44206200-44213400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:44206200-44213400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:44206200-44213600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:44206400-44206800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:44206400-44206800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr6:44206400-44207000	Enhancers	Stomach Smooth Muscle	stomach
39	chr6:44206400-44207000	Enhancers	Hela-S3	cervix
40	chr6:44206400-44207400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr6:44206400-44213000	Weak transcription	Brain Substantia Nigra	brain
42	chr6:44206400-44213200	Weak transcription	Adipose Nuclei	Adipose
43	chr6:44206400-44213200	Weak transcription	Stomach Mucosa	stomach
44	chr6:44206400-44213200	Weak transcription	HUVEC	blood vessel
45	chr6:44206400-44213200	Weak transcription	Osteobl	bone
46	chr6:44206600-44206800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:44206600-44206800	Strong transcription	Thymus	Thymus
48	chr6:44206600-44213200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:44206600-44213200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:44206600-44213400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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