Variant report

Variant	rs338668
Chromosome Location	chr5:68399604-68399605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68370456..68371966-chr5:68399176..68400870,2	K562	blood:
2	chr5:68394607..68396528-chr5:68398925..68400806,3	K562	blood:
3	chr5:68389331..68393521-chr5:68397846..68403936,9	K562	blood:

Variant related genes	Relation type
ENSG00000145740	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10056618	0.94[ASN][1000 genomes]
rs10434546	0.82[YRI][hapmap]
rs163191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs163193	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163194	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164391	0.94[ASN][1000 genomes]
rs164394	0.94[ASN][1000 genomes]
rs164396	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs164572	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs164577	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs164578	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs164579	0.80[CHB][hapmap];0.93[ASN][1000 genomes]
rs164580	0.92[ASN][1000 genomes]
rs164581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164710	0.96[ASN][1000 genomes]
rs164712	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs186790	0.92[ASN][1000 genomes]
rs187043	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240809	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs2447794	0.88[ASN][1000 genomes]
rs337253	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs337256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337259	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337262	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338678	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350110	0.83[ASN][1000 genomes]
rs350111	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs350112	0.88[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs351432	0.93[ASN][1000 genomes]
rs351444	0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs420228	0.94[ASN][1000 genomes]
rs454828	0.95[CHB][hapmap]
rs570884	0.94[ASN][1000 genomes]
rs6880864	0.89[YRI][hapmap]
rs688674	0.83[ASN][1000 genomes]
rs9291940	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3391099	chr5:68377245-68400350	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv881765	chr5:68379836-68448694	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68390600-68405600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68390800-68405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:68391000-68400600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:68391000-68401000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:68391000-68401000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:68391000-68402800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:68391000-68403000	Weak transcription	HSMMtube	muscle
8	chr5:68391000-68415200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:68391200-68401200	Weak transcription	Right Ventricle	heart
10	chr5:68391200-68402600	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:68391200-68405600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:68391200-68405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:68391200-68405600	Weak transcription	Psoas Muscle	Psoas
14	chr5:68391400-68401000	Weak transcription	Fetal Brain Female	brain
15	chr5:68391400-68401200	Weak transcription	Gastric	stomach
16	chr5:68391400-68401400	Weak transcription	Spleen	Spleen
17	chr5:68391400-68401600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:68391400-68402000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:68391400-68402600	Weak transcription	Brain Substantia Nigra	brain
20	chr5:68391400-68415800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:68391400-68428800	Weak transcription	Stomach Mucosa	stomach
22	chr5:68391400-68431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:68391600-68400800	Weak transcription	Primary B cells from cord blood	blood
24	chr5:68391600-68400800	Weak transcription	Fetal Lung	lung
25	chr5:68392000-68400800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:68392000-68401200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:68392000-68402800	Weak transcription	NHLF	lung
28	chr5:68392200-68427000	Weak transcription	Fetal Heart	heart
29	chr5:68392800-68400800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:68393000-68401000	Weak transcription	Brain Anterior Caudate	brain
31	chr5:68394200-68405200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:68395000-68419400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:68395000-68428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:68395200-68403800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:68395200-68405800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:68395400-68402800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:68395400-68413200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:68395600-68399800	Weak transcription	Left Ventricle	heart
39	chr5:68395600-68401200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:68395600-68401200	Weak transcription	Small Intestine	intestine
41	chr5:68395600-68401400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:68395600-68406400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:68396200-68399800	Weak transcription	Ovary	ovary
44	chr5:68396200-68406200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:68396400-68399800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:68396400-68400800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:68396400-68401000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:68396400-68401000	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:68396400-68401200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:68396400-68401200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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