Variant report

Variant	rs17041323
Chromosome Location	chr4:110984555-110984556
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	chr4:110984524-110984800	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110977785..110984731-chr4:111116105..111121044,7	MCF-7	breast:
2	chr4:110979668..110982097-chr4:110982494..110984694,2	MCF-7	breast:

Variant related genes	Relation type
ELOVL6	TF binding region
ENSG00000170522	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17041324	0.88[MEX][hapmap]
rs7662161	0.88[MEX][hapmap]
rs7684686	0.83[MEX][hapmap]
rs7690709	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap];0.82[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	nsv869392	chr4:110945459-111235071	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv1798003	chr4:110981611-110996948	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17041323	ALPK1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110964600-111004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:110965200-110986600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:110965400-110994200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:110970800-110995800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:110971800-110992800	Weak transcription	Fetal Stomach	stomach
6	chr4:110973000-110991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:110973000-111009200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:110973400-110992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:110974400-110990600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:110974600-110992600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:110977200-110985000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:110977200-110992400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:110977200-110992600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:110980200-110992600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:110980200-111004000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:110980800-110985200	Weak transcription	HepG2	liver
17	chr4:110980800-110990800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:110981000-110997000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:110981000-111004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:110981400-110991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:110981400-110992600	Weak transcription	Adipose Nuclei	Adipose
22	chr4:110981400-111006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:110981400-111009200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:110981600-110985400	Weak transcription	Fetal Intestine Large	intestine
25	chr4:110981600-110989400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:110982000-110984600	Weak transcription	Esophagus	oesophagus
27	chr4:110982000-110984600	Weak transcription	Gastric	stomach
28	chr4:110982000-110985000	Weak transcription	Right Atrium	heart
29	chr4:110982000-110985200	Weak transcription	Fetal Intestine Small	intestine
30	chr4:110982000-110988400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:110982000-110990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:110982000-110991800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:110982000-110993200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:110982000-110994400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:110982000-110994400	Weak transcription	Osteobl	bone
36	chr4:110982000-110995000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:110982000-110995800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:110982000-111003800	Weak transcription	NHEK	skin
39	chr4:110982200-110985400	Weak transcription	Stomach Mucosa	stomach
40	chr4:110982200-110994600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:110982400-110984600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:110982600-110984600	Weak transcription	Liver	Liver
43	chr4:110982600-110996200	Weak transcription	Dnd41	blood
44	chr4:110983600-110984600	Enhancers	Brain Substantia Nigra	brain
45	chr4:110983600-110984800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:110983600-110986000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:110983600-110988600	Weak transcription	K562	blood
48	chr4:110984000-110984800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:110984000-110985600	Enhancers	Brain Cingulate Gyrus	brain
50	chr4:110984000-110985600	Enhancers	Brain Hippocampus Middle	brain

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