Variant report

Variant	rs7174489
Chromosome Location	chr15:78302941-78302942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78302062..78306347-chr15:78307060..78310472,4	K562	blood:
2	chr15:78302785..78304913-chr15:78307547..78310258,2	K562	blood:
3	chr15:78294247..78296454-chr15:78301509..78303035,2	K562	blood:
4	chr15:78294247..78296927-chr15:78300006..78303035,3	K562	blood:

Variant related genes	Relation type
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004855	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519181	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11072716	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11631578	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11634607	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs11638311	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11852768	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12148365	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs12591418	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs12594823	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12901812	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12911332	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916362	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs1348257	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1442293	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1837913	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs1992470	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2028546	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2044099	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2241885	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867985	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs3803380	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs4395040	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs4886553	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4886554	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs4886994	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886996	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4886999	0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs4887000	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55704745	0.87[ASN][1000 genomes]
rs7166819	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7170746	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7173128	0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173473	0.80[ASN][1000 genomes]
rs8030713	0.93[ASN][1000 genomes]
rs8030873	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7174489	ISL2	cis	parietal	SCAN
rs7174489	CHRNA5	cis	parietal	SCAN
rs7174489	CLK3	cis	cerebellum	SCAN
rs7174489	HEXA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78283400-78305000	Weak transcription	K562	blood
2	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr15:78285400-78304400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:78288600-78303000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:78288600-78304400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
14	chr15:78288800-78304800	Weak transcription	Fetal Kidney	kidney
15	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr15:78289000-78309800	Strong transcription	Primary T cells from cord blood	blood
18	chr15:78289400-78309800	Strong transcription	Dnd41	blood
19	chr15:78293200-78309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:78293600-78310000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr15:78293800-78309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:78295600-78305600	Enhancers	Pancreas	Pancrea
23	chr15:78295800-78303200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:78295800-78303200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:78295800-78304400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:78295800-78304600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:78296000-78305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:78296200-78303000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:78296200-78316400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:78296400-78307800	Weak transcription	Hela-S3	cervix
32	chr15:78296600-78305000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:78296600-78307800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:78297400-78310800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:78297600-78310400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:78297800-78304400	Weak transcription	A549	lung
37	chr15:78297800-78305600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:78298400-78309600	Genic enhancers	Liver	Liver
39	chr15:78298600-78305200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr15:78298600-78309400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:78299000-78305000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:78299800-78303400	Strong transcription	Primary B cells from cord blood	blood
43	chr15:78299800-78304000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:78300200-78304400	Strong transcription	Fetal Intestine Large	intestine
45	chr15:78300200-78309000	Strong transcription	Aorta	Aorta
46	chr15:78300400-78304400	Strong transcription	Fetal Intestine Small	intestine
47	chr15:78300400-78305800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:78300600-78316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:78300800-78304400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:78300800-78304400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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