Variant report

Variant	rs3797368
Chromosome Location	chr5:118859958-118859959
allele	A/G
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	FOXA2	chr5:118859829-118861131	HepG2	liver:	n/a	chr5:118859883-118859895

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118828423..118830428-chr5:118858768..118861011,2	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10064000	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10077888	0.84[ASW][hapmap];0.85[CHB][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap]
rs10478422	0.95[CHB][hapmap];0.86[GIH][hapmap]
rs10478424	0.86[CHB][hapmap]
rs11205	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs11241507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1155777	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949608	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12187149	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1490756	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1509144	0.85[CHB][hapmap]
rs150938	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154596	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161853	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161854	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161855	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1620133	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1651227	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs165995	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs17145464	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1848554	1.00[CHB][hapmap];0.80[GIH][hapmap]
rs1995794	0.95[CHB][hapmap]
rs2451814	0.83[CEU][hapmap]
rs2451815	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2459727	0.91[ASN][1000 genomes]
rs246968	0.81[ASN][1000 genomes]
rs250303	1.00[LWK][hapmap]
rs257969	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257973	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs257979	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257980	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257983	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs257985	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2914210	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs32652	1.00[LWK][hapmap]
rs3797372	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813309	1.00[LWK][hapmap]
rs3822527	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3933553	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455991	0.90[CHB][hapmap]
rs457106	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs6897978	0.85[CHB][hapmap]
rs7716785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7721752	0.95[CHB][hapmap];0.86[GIH][hapmap]
rs924623	0.84[ASW][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];1.00[LWK][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	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882776	chr5:118859546-118915408	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118794800-118861200	Weak transcription	HSMM	muscle
2	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:118832400-118878200	Weak transcription	NH-A	brain
4	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:118833000-118860200	Weak transcription	Stomach Mucosa	stomach
6	chr5:118838000-118869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:118840200-118878400	Weak transcription	Psoas Muscle	Psoas
8	chr5:118841000-118880000	Weak transcription	Brain Germinal Matrix	brain
9	chr5:118841200-118880000	Weak transcription	A549	lung
10	chr5:118841400-118873200	Weak transcription	Fetal Brain Male	brain
11	chr5:118842200-118860200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:118845800-118868800	Weak transcription	Fetal Heart	heart
13	chr5:118846800-118860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:118846800-118862800	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:118846800-118878200	Weak transcription	NHLF	lung
16	chr5:118847000-118860000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:118847000-118863000	Weak transcription	NHDF-Ad	bronchial
18	chr5:118847000-118868000	Weak transcription	K562	blood
19	chr5:118847200-118873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:118847200-118877800	Weak transcription	Small Intestine	intestine
21	chr5:118847200-118878200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:118847200-118879800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:118847400-118861000	Weak transcription	Hela-S3	cervix
24	chr5:118847400-118863000	Weak transcription	HMEC	breast
25	chr5:118847400-118872000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:118847400-118873000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:118847400-118873200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:118847400-118873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:118847400-118875800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:118847400-118876000	Weak transcription	Colonic Mucosa	Colon
31	chr5:118847400-118878200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:118847400-118879800	Weak transcription	HSMMtube	muscle
33	chr5:118847600-118863400	Weak transcription	Brain Angular Gyrus	brain
34	chr5:118847600-118865000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:118847600-118873200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:118847600-118873400	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:118847600-118873600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:118847600-118877600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:118847600-118878200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:118847600-118879800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:118848000-118863400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:118848200-118863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:118848600-118863800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:118850000-118865600	Weak transcription	GM12878-XiMat	blood
45	chr5:118851200-118861200	Weak transcription	HUVEC	blood vessel
46	chr5:118851400-118860400	Weak transcription	Primary B cells from cord blood	blood
47	chr5:118851400-118861000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:118851600-118862800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:118851800-118876400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:118852000-118861200	Weak transcription	Fetal Thymus	thymus

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