Variant report

Variant	rs17748178
Chromosome Location	chr10:27139835-27139836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27135807..27140100-chr10:27147231..27150692,4	MCF-7	breast:
2	chr10:27137519..27140473-chr10:27148329..27151110,2	K562	blood:
3	chr10:27135636..27137752-chr10:27138213..27139984,2	MCF-7	breast:
4	chr10:27020685..27022973-chr10:27138065..27140730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12413383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12764628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774231	0.82[EUR][1000 genomes]
rs12779919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12780703	0.83[ASN][1000 genomes]
rs16927334	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17669895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747961	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094150	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182294	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35175791	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35531360	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5010875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5025734	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68021348	0.94[EUR][1000 genomes]
rs7091364	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7092950	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7094825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7096584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7916104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7920164	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17748178	ABI1	cis	cerebellum	SCAN
rs17748178	LYZL2	cis	parietal	SCAN
rs17748178	PDSS1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27095600-27148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:27111800-27147000	Weak transcription	Fetal Intestine Large	intestine
3	chr10:27119600-27147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:27120600-27142600	Weak transcription	HepG2	liver
5	chr10:27122600-27143400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:27123000-27145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:27124400-27146200	Weak transcription	Fetal Muscle Leg	muscle
8	chr10:27126600-27140000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr10:27128000-27143200	Weak transcription	Osteobl	bone
10	chr10:27129200-27142600	Weak transcription	Right Ventricle	heart
11	chr10:27129400-27142000	Weak transcription	Lung	lung
12	chr10:27129400-27146000	Weak transcription	Pancreas	Pancrea
13	chr10:27129400-27146400	Weak transcription	Gastric	stomach
14	chr10:27129400-27146600	Weak transcription	Esophagus	oesophagus
15	chr10:27129400-27147200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:27129400-27148200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr10:27129600-27146600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:27130000-27140000	Weak transcription	Fetal Lung	lung
19	chr10:27130000-27143800	Weak transcription	Brain Angular Gyrus	brain
20	chr10:27130200-27140400	Weak transcription	Brain Anterior Caudate	brain
21	chr10:27130200-27143000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:27130200-27143600	Weak transcription	NHDF-Ad	bronchial
23	chr10:27130200-27145600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr10:27130800-27145000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:27131200-27140200	Weak transcription	Small Intestine	intestine
26	chr10:27131200-27143200	Weak transcription	Stomach Mucosa	stomach
27	chr10:27131200-27143400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:27131200-27146000	Weak transcription	Right Atrium	heart
29	chr10:27131600-27145000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:27132000-27142800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:27133200-27140000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:27133600-27146400	Weak transcription	Psoas Muscle	Psoas
33	chr10:27133600-27148200	Weak transcription	Aorta	Aorta
34	chr10:27134000-27140000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr10:27134000-27140200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:27134000-27140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:27134000-27143200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:27134000-27143600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:27134000-27145000	Weak transcription	Fetal Thymus	thymus
40	chr10:27134000-27145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr10:27134000-27145400	Weak transcription	Adipose Nuclei	Adipose
42	chr10:27134000-27146800	Weak transcription	Brain Hippocampus Middle	brain
43	chr10:27134200-27140600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr10:27134200-27145400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:27134400-27140000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:27134400-27140000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr10:27134400-27140800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:27134400-27144200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr10:27134600-27143800	Weak transcription	Thymus	Thymus
50	chr10:27134800-27140800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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