Variant report

Variant	rs16846769
Chromosome Location	chr1:174190745-174190746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174190274..174193024-chr1:174230012..174232463,2	K562	blood:
2	chr1:174188636..174191430-chr1:174968395..174970624,2	K562	blood:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10489254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846815	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57425860	0.83[EUR][1000 genomes]
rs58525721	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58657641	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58911640	0.91[AFR][1000 genomes]
rs59061054	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59949376	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6668618	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698964	0.91[AFR][1000 genomes]
rs7516351	0.80[AFR][1000 genomes]
rs7549724	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS 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 lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846769	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs16846769	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174172800-174191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:174173200-174191400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:174174200-174200200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:174175400-174200200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:174176000-174190800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174176000-174222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:174176200-174191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:174176800-174222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:174177000-174191200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:174177200-174212000	Weak transcription	Lung	lung
11	chr1:174178600-174212200	Weak transcription	Psoas Muscle	Psoas
12	chr1:174178800-174190800	Weak transcription	Thymus	Thymus
13	chr1:174179200-174190800	Weak transcription	Dnd41	blood
14	chr1:174179400-174191000	Weak transcription	Fetal Intestine Small	intestine
15	chr1:174186200-174191200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:174186600-174191400	Weak transcription	Fetal Kidney	kidney
17	chr1:174186600-174216600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:174186800-174190800	Weak transcription	Left Ventricle	heart
19	chr1:174186800-174191000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:174186800-174191000	Weak transcription	Aorta	Aorta
21	chr1:174186800-174191200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:174186800-174191400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:174186800-174191400	Weak transcription	Adipose Nuclei	Adipose
24	chr1:174186800-174200400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:174186800-174200600	Weak transcription	Fetal Stomach	stomach
26	chr1:174186800-174200600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:174186800-174208000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:174186800-174212800	Weak transcription	Fetal Heart	heart
29	chr1:174186800-174213200	Weak transcription	Ovary	ovary
30	chr1:174186800-174217000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:174186800-174232000	Weak transcription	HSMMtube	muscle
32	chr1:174187000-174191200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:174187000-174199600	Weak transcription	A549	lung
34	chr1:174187000-174217000	Weak transcription	Pancreas	Pancrea
35	chr1:174187200-174190800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:174187400-174191000	Weak transcription	Osteobl	bone
37	chr1:174187400-174191200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:174187400-174200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:174187400-174208000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:174187600-174190800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:174187600-174190800	Weak transcription	Liver	Liver
42	chr1:174187600-174190800	Weak transcription	HMEC	breast
43	chr1:174187600-174191200	Weak transcription	HepG2	liver
44	chr1:174187600-174199800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:174187800-174190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:174187800-174191000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:174188200-174190800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:174188200-174190800	Weak transcription	NHEK	skin
49	chr1:174188400-174191000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:174188400-174191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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