Variant report

Variant	rs6700269
Chromosome Location	chr1:173424622-173424623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173423508..173426333-chr1:173427997..173430407,3	K562	blood:
2	chr1:173422565..173425228-chr1:173444418..173448207,4	K562	blood:
3	chr1:173419821..173425727-chr1:173444702..173448978,9	MCF-7	breast:
4	chr1:173422794..173425781-chr1:173831369..173833228,2	MCF-7	breast:
5	chr1:173414044..173416601-chr1:173422234..173425092,2	K562	blood:

Variant related genes	Relation type
ENSG00000270084	Chromatin interaction
ENSG00000117592	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10912620	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs11800778	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11809166	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11811598	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12075952	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12085083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562415	0.91[EUR][1000 genomes]
rs34619706	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35263596	0.89[ASN][1000 genomes]
rs3934577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55741047	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55816799	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57231379	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57262055	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57951216	0.88[ASN][1000 genomes]
rs59834293	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60302114	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60587131	0.91[ASN][1000 genomes]
rs60969203	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61061894	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61261546	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656413	0.92[YRI][hapmap]
rs6660804	0.81[YRI][hapmap]
rs6678064	0.93[CHB][hapmap]
rs6700499	0.91[EUR][1000 genomes]
rs6702339	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72726915	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72726936	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72726946	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726948	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72726949	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74126390	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7534736	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555324	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6700269		cis	Lymphoblastoid	GTEx
rs6700269	dJ383J4.3	cis	multi-tissue	Pritchard
rs6700269	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173387600-173429000	Weak transcription	Lung	lung
3	chr1:173391800-173429000	Weak transcription	Ovary	ovary
4	chr1:173400400-173429000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:173400600-173428800	Weak transcription	Fetal Stomach	stomach
6	chr1:173400800-173429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:173400800-173429000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:173401000-173428800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:173401000-173429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:173401000-173429000	Weak transcription	Left Ventricle	heart
11	chr1:173401800-173429000	Weak transcription	Primary B cells from cord blood	blood
12	chr1:173404200-173429000	Weak transcription	Adipose Nuclei	Adipose
13	chr1:173404200-173429000	Weak transcription	Right Ventricle	heart
14	chr1:173408800-173429000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:173408800-173429000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:173409000-173428800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:173409000-173428800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:173409000-173429200	Weak transcription	Aorta	Aorta
19	chr1:173411400-173427000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:173411600-173428800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:173413400-173429200	Weak transcription	Placenta	Placenta
22	chr1:173414600-173429000	Weak transcription	Thymus	Thymus
23	chr1:173415600-173429000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:173416000-173429000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:173416200-173429000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:173416400-173429000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:173416400-173430000	Weak transcription	Fetal Lung	lung
28	chr1:173416600-173429400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:173416800-173429000	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:173416800-173430000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:173416800-173430200	Weak transcription	GM12878-XiMat	blood
32	chr1:173418800-173429000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:173418800-173429000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:173418800-173429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:173419000-173429000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:173419000-173429200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:173419000-173432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:173419000-173439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:173419200-173428800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:173419400-173429000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:173419800-173429000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:173421000-173432200	Weak transcription	Fetal Brain Male	brain
43	chr1:173421400-173429000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:173421400-173429000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:173421400-173429200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:173421400-173429200	Weak transcription	HMEC	breast
47	chr1:173421400-173430000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:173421400-173434000	Weak transcription	Psoas Muscle	Psoas
49	chr1:173421600-173429000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:173421600-173429600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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