Variant report

Variant	rs17736496
Chromosome Location	chr6:5282118-5282119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5280760..5282906-chr6:5284734..5288197,3	K562	blood:
2	chr6:5275045..5278604-chr6:5280944..5282922,3	K562	blood:
3	chr6:5270189..5272095-chr6:5280821..5282645,2	K562	blood:
4	chr6:5260884..5263189-chr6:5279736..5282482,2	K562	blood:

Variant related genes	Relation type
ENSG00000214113	Chromatin interaction
ENSG00000145982	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11757927	1.00[GIH][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17140068	1.00[ASN][1000 genomes]
rs17140102	1.00[ASN][1000 genomes]
rs17736611	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17736761	0.80[AMR][1000 genomes]
rs17736905	1.00[GIH][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59548069	1.00[ASN][1000 genomes]
rs67285271	1.00[ASN][1000 genomes]
rs72813693	1.00[ASN][1000 genomes]
rs72813697	1.00[ASN][1000 genomes]
rs72813700	1.00[ASN][1000 genomes]
rs72815603	1.00[ASN][1000 genomes]
rs72815610	1.00[ASN][1000 genomes]
rs72815613	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72815615	1.00[ASN][1000 genomes]
rs72815618	1.00[ASN][1000 genomes]
rs72815620	1.00[ASN][1000 genomes]
rs72815643	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv275561	chr6:5281294-5285172	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17736496	LYRM4	cis	parietal	SCAN
rs17736496	FOXQ1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5262400-5287200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5262400-5302400	Weak transcription	Aorta	Aorta
3	chr6:5262600-5287200	Weak transcription	Esophagus	oesophagus
4	chr6:5262600-5287600	Weak transcription	Ovary	ovary
5	chr6:5262800-5287200	Weak transcription	Spleen	Spleen
6	chr6:5262800-5287400	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:5263000-5285200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:5263000-5287200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:5263000-5287400	Weak transcription	Fetal Stomach	stomach
10	chr6:5263000-5287800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:5263000-5301000	Weak transcription	Fetal Brain Male	brain
12	chr6:5263200-5287800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:5263400-5287400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:5263400-5287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:5263800-5291800	Weak transcription	Fetal Intestine Small	intestine
16	chr6:5267000-5290400	Weak transcription	HepG2	liver
17	chr6:5268000-5294400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:5273800-5285000	Weak transcription	Lung	lung
19	chr6:5274600-5287200	Weak transcription	Left Ventricle	heart
20	chr6:5274800-5287800	Weak transcription	NHEK	skin
21	chr6:5275000-5282200	Weak transcription	K562	blood
22	chr6:5275000-5290400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:5275200-5287400	Weak transcription	Psoas Muscle	Psoas
24	chr6:5275800-5285400	Weak transcription	Gastric	stomach
25	chr6:5276600-5287400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:5276600-5294000	Weak transcription	Fetal Intestine Large	intestine
27	chr6:5277200-5282200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:5277200-5283000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:5277400-5282400	Weak transcription	Pancreas	Pancrea
30	chr6:5277400-5287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:5278600-5287200	Weak transcription	Right Ventricle	heart
32	chr6:5279200-5287400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:5279200-5289800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:5279400-5282200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:5279400-5282200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:5279400-5282200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:5279400-5282400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:5279400-5288200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:5279400-5298200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:5280200-5283400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:5280400-5294000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:5280600-5282800	Enhancers	GM12878-XiMat	blood
43	chr6:5280600-5287200	Weak transcription	HMEC	breast
44	chr6:5280600-5289800	Weak transcription	Primary B cells from cord blood	blood
45	chr6:5280800-5289400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:5280800-5293200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:5280800-5308200	Weak transcription	Primary T cells from cord blood	blood
48	chr6:5281000-5285400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:5281000-5294400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:5281400-5287600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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