Variant report

Variant	rs17339110
Chromosome Location	chr7:108109611-108109612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108108975..108111125-chr7:108118694..108120937,2	K562	blood:
2	chr7:108091245..108093315-chr7:108108890..108111235,2	MCF-7	breast:
3	chr7:108102855..108105698-chr7:108109300..108111309,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10273997	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10278246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1034825	0.85[CEU][hapmap]
rs1034829	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs13221639	0.89[TSI][hapmap]
rs13244602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473131	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1859769	0.91[EUR][1000 genomes]
rs1859771	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859772	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859774	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859775	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs194585	0.92[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs194586	0.96[CEU][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2214916	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2284291	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2284292	0.83[EUR][1000 genomes]
rs2300053	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2396001	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3763462	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3815252	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[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];0.99[EUR][1000 genomes]
rs40846	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40849	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40856	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40890	0.93[EUR][1000 genomes]
rs40903	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs40916	0.83[YRI][hapmap]
rs40922	0.85[YRI][hapmap]
rs6466239	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6466240	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6966431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6976478	0.86[EUR][1000 genomes]
rs726471	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73426110	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800334	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7806223	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs917251	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9640707	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9785006	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	esv2753284	chr7:108105345-108130214	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17339110	LHFPL3	cis	parietal	SCAN
rs17339110	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
2	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:108101000-108119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:108101400-108116800	Weak transcription	Osteobl	bone
5	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
6	chr7:108102400-108137000	Weak transcription	NH-A	brain
7	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:108102600-108116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:108102600-108118200	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:108102800-108111000	Weak transcription	HSMM	muscle
11	chr7:108102800-108111200	Weak transcription	Adipose Nuclei	Adipose
12	chr7:108102800-108126400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
14	chr7:108103000-108111200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:108103200-108115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:108104200-108111200	Weak transcription	Left Ventricle	heart
17	chr7:108104400-108116400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:108104800-108117400	Weak transcription	Dnd41	blood
19	chr7:108105000-108116000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr7:108105600-108117800	Weak transcription	Thymus	Thymus
21	chr7:108105800-108111000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:108106000-108116800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:108106200-108150800	Weak transcription	NHLF	lung
25	chr7:108106400-108113000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:108106400-108117200	Weak transcription	Primary T cells from cord blood	blood
27	chr7:108106600-108127600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:108106800-108130000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
30	chr7:108108200-108111400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:108108200-108111600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:108108400-108113400	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:108108600-108122000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:108108800-108118200	Weak transcription	Right Ventricle	heart
35	chr7:108108800-108118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:108109000-108111200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:108109000-108111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:108109000-108111400	Weak transcription	Liver	Liver
39	chr7:108109000-108112600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:108109000-108117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:108109000-108119200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:108109000-108126400	Weak transcription	HUVEC	blood vessel
43	chr7:108109000-108129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:108109200-108110000	Enhancers	Primary B cells from peripheral blood	blood
48	chr7:108109200-108111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:108109200-108114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:108109200-108117000	Weak transcription	Rectal Mucosa Donor 29	rectum

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