Variant report

Variant	rs9456644
Chromosome Location	chr6:161655011-161655012
allele	C/T
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	NFIC	chr6:161654959-161655861	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161411531..161413327-chr6:161653025..161655728,2	K562	blood:
2	chr6:161654520..161656556-chr6:161665296..161667922,2	K562	blood:

Variant related genes	Relation type
AGPAT4	TF binding region
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11756702	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970608	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17551959	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627837	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775164	0.91[EUR][1000 genomes]
rs9295144	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458163	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9458172	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv949397	chr6:161592100-161812932	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2752091	chr6:161592100-161855785	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1029727	chr6:161607680-161814295	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1030623	chr6:161611170-161796985	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv538494	chr6:161611170-161796985	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers 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	3 gene(s)	inside rSNPs	diseases
8	nsv886818	chr6:161629323-161723705	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv533149	chr6:161653240-161769727	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9456644	AKR7A3	trans	parietal	SCAN
rs9456644	TCP1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161636600-161656000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:161638200-161693800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:161638600-161668000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:161639000-161666200	Weak transcription	Aorta	Aorta
5	chr6:161639200-161664400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:161647200-161663200	Weak transcription	Thymus	Thymus
7	chr6:161648000-161656800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:161648000-161660600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:161648800-161656800	Weak transcription	Right Ventricle	heart
10	chr6:161649400-161657400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:161649400-161662800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:161649600-161693800	Weak transcription	Right Atrium	heart
13	chr6:161650000-161662800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:161650200-161656800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:161650400-161658000	Enhancers	Brain Substantia Nigra	brain
16	chr6:161650800-161655200	Weak transcription	Fetal Lung	lung
17	chr6:161651000-161655200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:161651000-161655200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:161651000-161655200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:161651000-161655200	Weak transcription	HSMMtube	muscle
21	chr6:161651000-161655400	Weak transcription	Left Ventricle	heart
22	chr6:161651000-161655600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:161651000-161656800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:161651000-161658800	Weak transcription	Esophagus	oesophagus
25	chr6:161651000-161663400	Weak transcription	Lung	lung
26	chr6:161651000-161677000	Weak transcription	Spleen	Spleen
27	chr6:161651200-161655400	Weak transcription	HUVEC	blood vessel
28	chr6:161651200-161666000	Weak transcription	Primary T cells from cord blood	blood
29	chr6:161653000-161655400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:161653200-161655200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:161653200-161655200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:161653200-161655400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:161653200-161656800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:161653200-161664200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr6:161653400-161656600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:161653400-161659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:161653600-161655200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:161653600-161656800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:161653600-161657600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:161653600-161658200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:161653600-161660800	Weak transcription	Fetal Kidney	kidney
42	chr6:161653800-161656600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:161653800-161656600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:161653800-161657400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:161653800-161658200	Enhancers	Brain Germinal Matrix	brain
46	chr6:161653800-161659600	Enhancers	Fetal Heart	heart
47	chr6:161653800-161693800	Weak transcription	Primary B cells from cord blood	blood
48	chr6:161654000-161655400	Weak transcription	Ovary	ovary
49	chr6:161654000-161655600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:161654000-161664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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