Variant report

Variant	rs11070241
Chromosome Location	chr15:40284802-40284803
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	chr15:40284232..40286677-chr15:40295570..40297974,2	K562	blood:
2	chr15:40283947..40287472-chr15:40288447..40291993,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11070242	0.81[ASN][1000 genomes]
rs11633992	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12050884	0.85[EUR][1000 genomes]
rs12591670	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12901892	0.84[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1436276	0.82[JPT][hapmap]
rs16970132	0.83[JPT][hapmap]
rs16970168	0.88[JPT][hapmap]
rs2279580	0.88[JPT][hapmap]
rs2291623	0.88[JPT][hapmap]
rs2291625	0.81[ASN][1000 genomes]
rs2307105	0.83[JPT][hapmap]
rs28714278	0.81[EUR][1000 genomes]
rs2898974	0.88[JPT][hapmap]
rs479500	0.82[JPT][hapmap]
rs509200	0.82[JPT][hapmap]
rs510949	0.83[JPT][hapmap]
rs514152	0.83[JPT][hapmap]
rs518802	0.81[JPT][hapmap]
rs536503	0.83[JPT][hapmap]
rs548091	0.83[JPT][hapmap]
rs7178419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[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];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11070241	GCHFR	cis	cerebellum	SCAN
rs11070241	EIF2AK4	cis	cerebellum	SCAN
rs11070241	CHAC1	cis	cerebellum	SCAN
rs11070241	MEIS2	cis	parietal	SCAN
rs11070241	EIF2AK4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:40236600-40303000	Weak transcription	Small Intestine	intestine
3	chr15:40249000-40304800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:40250000-40294800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:40250200-40299600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:40260800-40303400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:40262600-40293800	Weak transcription	Stomach Mucosa	stomach
8	chr15:40269000-40293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:40269000-40293200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:40269600-40295600	Weak transcription	Fetal Heart	heart
11	chr15:40269800-40285400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:40276400-40295600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:40277600-40287400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40277600-40288400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:40277600-40294600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40277600-40303600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:40277600-40303800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:40277600-40304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:40277800-40285800	Strong transcription	Brain Cingulate Gyrus	brain
22	chr15:40277800-40286000	Strong transcription	Brain Anterior Caudate	brain
23	chr15:40277800-40286600	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:40277800-40286600	Strong transcription	A549	lung
25	chr15:40277800-40286600	Strong transcription	Dnd41	blood
26	chr15:40277800-40286600	Strong transcription	HSMM	muscle
27	chr15:40277800-40286600	Strong transcription	NHDF-Ad	bronchial
28	chr15:40277800-40286600	Strong transcription	NHEK	skin
29	chr15:40277800-40286600	Strong transcription	Osteobl	bone
30	chr15:40277800-40286800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr15:40277800-40287000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:40277800-40287600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:40277800-40287800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr15:40277800-40288000	Strong transcription	HMEC	breast
35	chr15:40277800-40288200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:40277800-40288400	Strong transcription	NH-A	brain
37	chr15:40277800-40288600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:40277800-40288800	Strong transcription	Placenta	Placenta
39	chr15:40277800-40288800	Strong transcription	Fetal Stomach	stomach
40	chr15:40277800-40290200	Strong transcription	Ovary	ovary
41	chr15:40277800-40290200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:40277800-40290800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr15:40277800-40290800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:40277800-40290800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:40277800-40291000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:40277800-40291200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:40277800-40291200	Strong transcription	Adipose Nuclei	Adipose
48	chr15:40277800-40291200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:40277800-40291400	Strong transcription	Primary T cells from cord blood	blood
50	chr15:40277800-40291400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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