Variant report

Variant	rs10903246
Chromosome Location	chr5:179447755-179447756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179446297..179447924-chr5:179497601..179500214,2	MCF-7	breast:
2	chr5:179447316..179449244-chr5:179516942..179519007,2	MCF-7	breast:
3	chr5:179447593..179449240-chr5:179494400..179496143,2	MCF-7	breast:
4	chr5:179439567..179442502-chr5:179447690..179450010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198995	Chromatin interaction
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10036834	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10045755	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10051632	0.85[EUR][1000 genomes]
rs10061480	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068529	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068594	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10078977	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479455	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479557	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1102190	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12153541	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12653944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656219	0.89[CHD][hapmap]
rs17079966	0.81[GIH][hapmap]
rs173562	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs185076	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs193718	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs248257	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248258	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248316	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248320	0.81[GIH][hapmap]
rs27013	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs27014	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27016	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27017	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs27018	0.81[GIH][hapmap]
rs27019	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28011	0.85[CHD][hapmap]
rs35928331	0.86[ASN][1000 genomes]
rs3797763	0.81[GIH][hapmap]
rs3797764	0.81[GIH][hapmap]
rs394588	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4129403	0.81[GIH][hapmap]
rs4130025	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs418384	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4340879	0.81[CEU][hapmap]
rs4466125	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs449511	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700855	0.88[CHD][hapmap]
rs55734821	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62405020	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405021	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871596	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6888883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7706570	0.81[CEU][hapmap]
rs857181	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs857182	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857183	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs857189	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs864482	0.81[GIH][hapmap]
rs9329096	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10903246	CLTB	cis	parietal	SCAN
rs10903246	TRIM7	cis	parietal	SCAN
rs10903246	RASGEF1C	cis	cerebellum	SCAN
rs10903246	ZFP2	cis	parietal	SCAN
rs10903246	MAML1	cis	parietal	SCAN
rs10903246	LMAN2	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:179429400-179452800	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:179430000-179453000	Weak transcription	NH-A	brain
11	chr5:179430600-179462400	Weak transcription	HepG2	liver
12	chr5:179434800-179448200	Weak transcription	Fetal Heart	heart
13	chr5:179435200-179448800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:179435400-179453400	Weak transcription	Right Atrium	heart
15	chr5:179435800-179454600	Weak transcription	K562	blood
16	chr5:179436200-179449200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:179436200-179450600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:179439200-179452600	Weak transcription	HUVEC	blood vessel
21	chr5:179439600-179453400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:179439800-179448000	Weak transcription	Primary B cells from cord blood	blood
23	chr5:179440000-179451000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:179440000-179453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:179440200-179457600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:179440200-179462600	Weak transcription	Fetal Intestine Large	intestine
27	chr5:179440600-179462400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:179442600-179448800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179443400-179452200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:179443800-179451200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179444000-179452000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:179444200-179453400	Weak transcription	Brain Angular Gyrus	brain
33	chr5:179444600-179448800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:179444600-179449200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:179445400-179447800	Strong transcription	Fetal Muscle Leg	muscle
36	chr5:179445400-179447800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr5:179445400-179449200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:179445800-179449800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:179446000-179448800	Weak transcription	Brain Substantia Nigra	brain
40	chr5:179446000-179451800	Weak transcription	Psoas Muscle	Psoas
41	chr5:179446000-179452600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:179446000-179462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:179446400-179447800	Strong transcription	Left Ventricle	heart
44	chr5:179446400-179449000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:179446400-179449200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr5:179446600-179448800	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:179446600-179450200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:179446600-179450400	Weak transcription	Adipose Nuclei	Adipose
49	chr5:179446800-179447800	Strong transcription	Liver	Liver
50	chr5:179446800-179447800	Strong transcription	Ovary	ovary

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