Variant report

Variant	rs10935518
Chromosome Location	chr3:98615611-98615612
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	chr3:98598356-98618077	U87	brain:	n/a	n/a
2	POLR2A	chr3:98601861-98618157	U87	brain:	n/a	n/a
3	POLR2A	chr3:98601867-98618131	U87	brain:	n/a	n/a
4	POLR2A	chr3:98615562-98615942	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:98592632-98618071	U87	brain:	n/a	n/a
6	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98615054..98618037-chr3:98618914..98621947,4	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs10935542	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.91[ASN][1000 genomes]
rs11716000	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716007	0.91[ASN][1000 genomes]
rs11716281	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914591	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11916285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11918243	0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11920327	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.91[ASN][1000 genomes]
rs12203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1471588	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17210963	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs17212369	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs17278047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278278	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	0.94[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1827158	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772100	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55650073	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55662129	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.91[EUR][1000 genomes]
rs56290036	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322058	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276885	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276888	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276909	0.88[ASN][1000 genomes]
rs6440159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6440253	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66517942	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.89[EUR][1000 genomes]
rs73136045	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73136048	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73136057	0.88[EUR][1000 genomes]
rs73136060	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73138004	0.91[EUR][1000 genomes]
rs73138027	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8179927	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs982291	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10935518	OR5K2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
3	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
5	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
7	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
8	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
9	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:98609000-98615800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:98610400-98615800	Transcr. at gene 5' and 3'	NH-A	brain
12	chr3:98610400-98616600	Transcr. at gene 5' and 3'	A549	lung
13	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
15	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:98611200-98617000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:98611600-98616600	Weak transcription	Fetal Lung	lung
20	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
23	chr3:98612600-98616000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:98612600-98616000	Transcr. at gene 5' and 3'	HMEC	breast
25	chr3:98612600-98618400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:98612800-98617400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:98612800-98618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:98613000-98616000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:98613000-98616200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
30	chr3:98613000-98617600	Weak transcription	Adipose Nuclei	Adipose
31	chr3:98613000-98618400	Weak transcription	GM12878-XiMat	blood
32	chr3:98613000-98618600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:98613000-98618600	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:98613000-98618600	Weak transcription	HSMMtube	muscle
35	chr3:98613200-98616000	Weak transcription	HepG2	liver
36	chr3:98613200-98616200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:98613200-98616200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:98613200-98618600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:98613200-98618800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
41	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:98613400-98616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:98613400-98616600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:98613400-98617200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:98613400-98618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:98613600-98616000	Weak transcription	HSMM	muscle
47	chr3:98613600-98616200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:98613600-98616400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:98613600-98616800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:98613600-98617200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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