Variant report

Variant	rs17362839
Chromosome Location	chr2:9754439-9754440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:9750980-9757087	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:9752087-9755033	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:42142647..42144954-chr2:9753163..9755825,2	MCF-7	breast:
2	chr2:9694040..9697595-chr2:9752237..9755817,4	MCF-7	breast:
3	chr2:9752399..9758466-chr2:9767981..9772630,10	MCF-7	breast:
4	chr2:9692463..9694432-chr2:9752498..9755143,2	MCF-7	breast:
5	chr2:9752582..9755080-chr2:9755247..9757680,2	MCF-7	breast:
6	chr2:9749693..9751303-chr2:9753003..9754631,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207086	TF binding region
ENSG00000161654	Chromatin interaction
ENSG00000134308	Chromatin interaction
ENSG00000207086	Chromatin interaction
ENSG00000271855	Chromatin interaction
ENSG00000151694	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10495571	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495572	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495573	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11676903	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11692112	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11694314	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16867083	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17362734	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17362902	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453675	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453724	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17453752	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55883249	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372340	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57234614	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57407838	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60319753	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60726087	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119391	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62119392	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62119393	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119422	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62119423	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62119428	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119429	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119431	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119432	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62119433	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17362839	IAH1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9741400-9760000	Weak transcription	Fetal Kidney	kidney
3	chr2:9742200-9757000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:9742800-9757800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9744600-9755200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:9744800-9766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:9747800-9760200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:9748000-9757000	Enhancers	Brain Hippocampus Middle	brain
9	chr2:9748600-9755000	Weak transcription	Fetal Stomach	stomach
10	chr2:9748600-9756400	Enhancers	Brain Substantia Nigra	brain
11	chr2:9748600-9765600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:9748600-9766600	Weak transcription	Aorta	Aorta
13	chr2:9748600-9767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:9748800-9758800	Weak transcription	Thymus	Thymus
15	chr2:9748800-9761200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:9748800-9763400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:9749000-9755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:9749000-9756800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:9749000-9757800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:9749000-9764600	Weak transcription	Lung	lung
21	chr2:9749000-9769200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:9749200-9764000	Weak transcription	Fetal Brain Male	brain
23	chr2:9749200-9768000	Weak transcription	Stomach Mucosa	stomach
24	chr2:9749400-9762800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:9749600-9758000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:9749600-9768200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:9750000-9755800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:9750000-9755800	Strong transcription	Dnd41	blood
29	chr2:9750000-9758000	Weak transcription	HUVEC	blood vessel
30	chr2:9750200-9758400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:9750200-9758600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:9750400-9756000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:9750800-9756400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:9751000-9757000	Enhancers	Colon Smooth Muscle	Colon
35	chr2:9751000-9757000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:9751000-9759000	Genic enhancers	A549	lung
37	chr2:9751200-9754800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:9751200-9755200	Strong transcription	Primary B cells from cord blood	blood
39	chr2:9751400-9755000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:9751600-9755000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:9751600-9756000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:9751600-9758800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:9751800-9756200	Enhancers	Fetal Heart	heart
44	chr2:9751800-9758800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:9752200-9757000	Enhancers	Brain Angular Gyrus	brain
46	chr2:9752200-9757200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:9752200-9757800	Weak transcription	Left Ventricle	heart
48	chr2:9752200-9762200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:9752200-9768200	Weak transcription	Colonic Mucosa	Colon
50	chr2:9752400-9754600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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