Variant report

Variant	rs6435401
Chromosome Location	chr2:208829527-208829528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208824191..208827889-chr2:208829117..208831257,3	K562	blood:
2	chr2:208824191..208827889-chr2:208829117..208831257,4	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10192065	0.86[JPT][hapmap]
rs10221788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037416	0.89[JPT][hapmap]
rs10497892	0.86[JPT][hapmap]
rs10932217	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674933	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676872	0.86[JPT][hapmap]
rs11679492	0.86[JPT][hapmap]
rs11687058	0.86[JPT][hapmap]
rs11692908	0.86[JPT][hapmap]
rs13006024	0.82[JPT][hapmap]
rs13025100	0.86[JPT][hapmap]
rs13402422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044971	0.86[JPT][hapmap]
rs2123294	0.82[JPT][hapmap]
rs2362783	0.86[JPT][hapmap]
rs3795911	0.82[JPT][hapmap]
rs3795912	0.82[JPT][hapmap]
rs4021953	0.86[JPT][hapmap]
rs4507086	0.86[JPT][hapmap]
rs4673377	0.86[JPT][hapmap]
rs62190860	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712527	0.86[JPT][hapmap]
rs6733857	0.82[JPT][hapmap]
rs6741366	0.86[JPT][hapmap]
rs7355275	0.81[JPT][hapmap]
rs7570588	0.86[JPT][hapmap]
rs7593972	0.86[JPT][hapmap]
rs7595734	0.86[JPT][hapmap]
rs7595823	0.81[JPT][hapmap]
rs896636	0.86[JPT][hapmap]
rs930746	0.86[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6435401	INO80D	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208796000-208835200	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:208798800-208834200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:208810400-208833600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:208810400-208841000	Weak transcription	Fetal Lung	lung
5	chr2:208811200-208835200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:208815400-208835400	Weak transcription	Right Ventricle	heart
7	chr2:208815400-208840800	Weak transcription	Ovary	ovary
8	chr2:208816600-208834000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:208817000-208833000	Weak transcription	Psoas Muscle	Psoas
10	chr2:208817200-208834600	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:208819200-208834000	Weak transcription	Stomach Mucosa	stomach
12	chr2:208825200-208841400	Weak transcription	Aorta	Aorta
13	chr2:208825600-208841400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:208826600-208841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:208826800-208840800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:208827200-208841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:208827200-208841400	Weak transcription	Pancreas	Pancrea
18	chr2:208827400-208834000	Weak transcription	HepG2	liver
19	chr2:208827400-208834800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:208827400-208835200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:208827400-208841400	Weak transcription	Left Ventricle	heart
22	chr2:208827400-208841400	Weak transcription	Lung	lung
23	chr2:208827400-208857400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:208827600-208831800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:208827600-208832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:208827600-208832400	Weak transcription	Fetal Brain Female	brain
27	chr2:208827600-208834200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:208827600-208834800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:208827800-208840800	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:208828000-208833000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:208828000-208834400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:208828000-208834800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:208828000-208834800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:208828000-208840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:208828000-208841000	Weak transcription	Fetal Thymus	thymus
36	chr2:208828200-208831800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:208828200-208831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:208828200-208833400	Weak transcription	Fetal Intestine Small	intestine
39	chr2:208828200-208834600	Weak transcription	Primary B cells from cord blood	blood
40	chr2:208828200-208835000	Weak transcription	Primary T cells from cord blood	blood
41	chr2:208828200-208838600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:208828200-208838600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:208828200-208840400	Weak transcription	Thymus	Thymus
44	chr2:208828200-208841400	Weak transcription	Dnd41	blood
45	chr2:208828400-208834200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:208828800-208832000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:208829000-208829600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:208829200-208832200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:208829400-208830800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:208829400-208832000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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