Variant report

Variant	rs11258317
Chromosome Location	chr10:6407737-6407738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6407311..6409448-chr10:6446152..6447736,2	MCF-7	breast:
2	chr10:6273175..6275381-chr10:6405443..6408001,2	MCF-7	breast:
3	chr10:6364749..6366254-chr10:6407399..6408916,2	MCF-7	breast:
4	chr10:6244771..6246608-chr10:6406133..6408869,3	MCF-7	breast:
5	chr10:6405295..6407901-chr10:6440170..6443280,3	MCF-7	breast:
6	chr10:6400244..6402480-chr10:6406686..6408396,2	MCF-7	breast:
7	chr10:6338433..6344348-chr10:6402915..6408706,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2387399	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2516624	1.00[CHB][hapmap]
rs681699	1.00[CHB][hapmap]
rs947473	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv5676	chr10:6381200-6428950	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv50	chr10:6393063-6422816	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1044870	chr10:6393260-6419462	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1047165	chr10:6393471-6411469	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1051840	chr10:6398966-6411469	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv508567	chr10:6407682-6427637	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1808540	chr10:6407737-6419765	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder and schizophrenia	20889312	GWAS catalog

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6396800-6410800	Weak transcription	Aorta	Aorta
2	chr10:6403400-6410200	Weak transcription	Ovary	ovary
3	chr10:6406200-6409800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr10:6406800-6407800	Enhancers	Liver	Liver
5	chr10:6406800-6407800	Enhancers	Fetal Heart	heart
6	chr10:6406800-6408000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:6406800-6408000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:6406800-6408000	Enhancers	A549	lung
9	chr10:6406800-6408200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:6406800-6408600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr10:6406800-6409200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:6407000-6407800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr10:6407000-6407800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:6407000-6408000	Enhancers	Stomach Mucosa	stomach
15	chr10:6407000-6408000	Enhancers	HepG2	liver
16	chr10:6407000-6408400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr10:6407000-6408400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:6407000-6408400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:6407000-6408600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr10:6407000-6409000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr10:6407000-6410400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr10:6407200-6407800	Enhancers	HSMMtube	muscle
23	chr10:6407200-6408800	Weak transcription	Pancreas	Pancrea
24	chr10:6407400-6408000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr10:6407400-6408000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr10:6407400-6408200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr10:6407400-6422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr10:6407600-6407800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr10:6407600-6407800	Enhancers	Fetal Intestine Small	intestine

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