Variant report

Variant	rs6435402
Chromosome Location	chr2:208887624-208887625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:208883791..208887954-chr2:208888473..208891537,5	MCF-7	breast:
2	chr2:208627808..208629541-chr2:208887379..208889271,2	MCF-7	breast:
3	chr2:208633416..208635575-chr2:208887303..208890126,3	MCF-7	breast:
4	chr2:208883906..208887647-chr2:208888508..208891752,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178385	Chromatin interaction
ENSG00000163251	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10497895	0.86[CEU][hapmap];0.90[GIH][hapmap]
rs10932224	0.80[EUR][1000 genomes]
rs11676872	0.90[LWK][hapmap]
rs12464255	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs12465052	0.86[CEU][hapmap]
rs12465292	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12471242	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13431014	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1452521	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17459574	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17459758	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537670	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17538061	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs2362787	0.80[EUR][1000 genomes]
rs28463196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4502388	0.93[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62190863	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62190896	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190898	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190900	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62190904	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62190905	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62192772	0.87[EUR][1000 genomes]
rs62192773	0.87[EUR][1000 genomes]
rs6740362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969822	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72981543	0.82[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7588162	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs930745	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6435402	SNORA41	cis	cerebellum	SCAN
rs6435402	CREB1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208854200-208889400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:208857200-208888000	Weak transcription	Fetal Brain Male	brain
3	chr2:208865200-208889000	Weak transcription	Brain Substantia Nigra	brain
4	chr2:208866400-208888200	Weak transcription	Ovary	ovary
5	chr2:208866600-208888200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:208866600-208889000	Weak transcription	Fetal Stomach	stomach
7	chr2:208866600-208889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:208866800-208888200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:208866800-208889400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:208867000-208888200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:208867400-208887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:208867400-208889000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:208867400-208889200	Weak transcription	Primary T cells from cord blood	blood
14	chr2:208871800-208889000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:208871800-208889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:208872400-208888200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:208875600-208889000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:208877600-208888200	Weak transcription	Psoas Muscle	Psoas
19	chr2:208877800-208888600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:208878600-208889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:208878800-208888200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:208878800-208889000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:208879000-208888000	Weak transcription	Lung	lung
24	chr2:208879000-208888200	Weak transcription	Pancreas	Pancrea
25	chr2:208879000-208888400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:208879000-208889400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:208879000-208889400	Weak transcription	Fetal Kidney	kidney
28	chr2:208879200-208888200	Weak transcription	Left Ventricle	heart
29	chr2:208879200-208889000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:208879400-208889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:208879600-208889200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:208880000-208889000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:208880600-208889000	Weak transcription	HepG2	liver
34	chr2:208880800-208888200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:208881200-208889600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:208882400-208889600	Weak transcription	Fetal Thymus	thymus
37	chr2:208882600-208889400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:208882600-208889600	Weak transcription	Small Intestine	intestine
39	chr2:208882800-208888200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:208882800-208889000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:208882800-208889400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:208882800-208889400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:208882800-208889600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:208882800-208889600	Weak transcription	Aorta	Aorta
45	chr2:208883000-208888400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:208883400-208888200	Weak transcription	Right Atrium	heart
47	chr2:208883400-208888200	Weak transcription	Spleen	Spleen
48	chr2:208883400-208889000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:208883600-208888000	Weak transcription	Adipose Nuclei	Adipose
50	chr2:208883600-208888600	Weak transcription	Rectal Mucosa Donor 29	rectum

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