Variant report

Variant	rs13196590
Chromosome Location	chr6:109561918-109561919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109559579..109562142-chr6:109563967..109566714,2	MCF-7	breast:
2	chr6:109560239..109561948-chr6:109701485..109704376,3	MCF-7	breast:
3	chr6:109561439..109564870-chr6:109795296..109799146,3	K562	blood:
4	chr6:109550909..109553791-chr6:109560961..109563998,3	K562	blood:
5	chr6:109561446..109564141-chr6:109698737..109700867,2	K562	blood:
6	chr6:109561591..109563297-chr6:109615936..109618604,2	K562	blood:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1008084	0.84[CEU][hapmap]
rs11153161	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153166	0.80[TSI][hapmap]
rs11153167	0.80[TSI][hapmap]
rs11153168	0.87[CEU][hapmap]
rs11964178	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11966072	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs1260593	0.82[CEU][hapmap]
rs1260595	0.84[CEU][hapmap]
rs1260596	0.87[CEU][hapmap]
rs1271693	0.89[ASN][1000 genomes]
rs13196219	0.91[CEU][hapmap]
rs13200047	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs13202939	0.83[CEU][hapmap]
rs13211313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13211944	0.95[ASN][1000 genomes]
rs1341271	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs1341272	0.84[CEU][hapmap]
rs1741923	0.97[ASN][1000 genomes]
rs1741930	0.84[CEU][hapmap]
rs1761608	0.84[CEU][hapmap]
rs2884036	0.83[CEU][hapmap]
rs34774766	0.97[ASN][1000 genomes]
rs351716	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs351717	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs351718	0.99[ASN][1000 genomes]
rs351719	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs351720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs351721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs351722	0.99[ASN][1000 genomes]
rs351723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs351724	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs351725	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs351726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs351727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs351728	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs351731	0.95[ASN][1000 genomes]
rs351732	0.94[ASN][1000 genomes]
rs351735	0.88[ASN][1000 genomes]
rs351736	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs351737	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs351742	0.83[CEU][hapmap]
rs351744	0.94[ASN][1000 genomes]
rs351746	0.97[ASN][1000 genomes]
rs351747	0.97[ASN][1000 genomes]
rs351750	0.97[ASN][1000 genomes]
rs351751	0.98[ASN][1000 genomes]
rs353052	0.88[ASN][1000 genomes]
rs368467	0.84[CEU][hapmap]
rs371960	0.83[CEU][hapmap]
rs377436	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs386696	0.83[CEU][hapmap]
rs388526	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396000	0.84[CEU][hapmap]
rs396635	0.97[ASN][1000 genomes]
rs399561	0.83[CEU][hapmap]
rs408944	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs410449	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs412754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs418093	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419106	0.84[CEU][hapmap]
rs421790	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422113	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs427960	0.83[CEU][hapmap]
rs429534	0.97[ASN][1000 genomes]
rs4301336	0.83[CEU][hapmap]
rs436880	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs442405	0.83[CEU][hapmap]
rs446974	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs448496	0.98[ASN][1000 genomes]
rs449736	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs449850	0.83[CEU][hapmap]
rs455839	0.83[CEU][hapmap]
rs458185	0.83[CEU][hapmap]
rs458740	0.80[CEU][hapmap]
rs459956	0.82[CEU][hapmap]
rs461487	0.82[CEU][hapmap]
rs463503	0.81[CEU][hapmap]
rs463916	0.83[CEU][hapmap]
rs566164	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs59673	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs6568571	0.88[CEU][hapmap]
rs6919423	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925339	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs7748918	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs830552	0.98[ASN][1000 genomes]
rs830553	0.86[EUR][1000 genomes]
rs830554	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs830556	0.98[ASN][1000 genomes]
rs9320278	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374080	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs9374081	0.91[CEU][hapmap]
rs9384701	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9386774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9386775	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9386796	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs9400272	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs9400273	0.84[CEU][hapmap]
rs9400276	0.83[CEU][hapmap]
rs9487048	0.83[CEU][hapmap]

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	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13196590	RAB40AL	trans	parietal	SCAN
rs13196590	ATG5	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109556800-109562800	Enhancers	Primary hematopoietic stem cells	blood
2	chr6:109556800-109564200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:109557200-109562000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:109557200-109565000	Enhancers	NHDF-Ad	bronchial
5	chr6:109557400-109562000	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:109557400-109562200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:109557600-109562000	Enhancers	Stomach Mucosa	stomach
8	chr6:109557600-109565200	Enhancers	Hela-S3	cervix
9	chr6:109558000-109562000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:109558200-109565000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:109558200-109565200	Enhancers	Osteobl	bone
12	chr6:109558200-109572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:109558600-109562800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:109558800-109566400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:109559000-109563400	Enhancers	Primary B cells from cord blood	blood
16	chr6:109559000-109564000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:109559000-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:109559200-109564200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:109559400-109563600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr6:109559400-109563600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:109559600-109562600	Enhancers	Adipose Nuclei	Adipose
22	chr6:109560000-109562200	Enhancers	Brain Angular Gyrus	brain
23	chr6:109560000-109562200	Enhancers	Brain Substantia Nigra	brain
24	chr6:109560000-109562600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:109560000-109563000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:109560400-109562000	Enhancers	Brain Hippocampus Middle	brain
27	chr6:109560400-109562000	Enhancers	Fetal Intestine Large	intestine
28	chr6:109560400-109562000	Enhancers	Fetal Intestine Small	intestine
29	chr6:109560400-109562000	Enhancers	Psoas Muscle	Psoas
30	chr6:109560400-109562200	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:109560400-109562600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:109560400-109563600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr6:109560400-109564200	Enhancers	HSMM	muscle
34	chr6:109560600-109562000	Enhancers	Fetal Stomach	stomach
35	chr6:109560800-109562000	Flanking Active TSS	HepG2	liver
36	chr6:109561000-109562000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:109561000-109562000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:109561000-109562000	Enhancers	Lung	lung
39	chr6:109561200-109562000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:109561200-109562400	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr6:109561400-109562000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:109561400-109562000	Enhancers	Fetal Muscle Trunk	muscle
43	chr6:109561400-109562200	Enhancers	Fetal Muscle Leg	muscle
44	chr6:109561600-109562000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:109561600-109562000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:109561600-109562000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr6:109561600-109562000	Enhancers	Placenta	Placenta
48	chr6:109561600-109562000	Enhancers	Fetal Thymus	thymus
49	chr6:109561600-109562000	Enhancers	Left Ventricle	heart
50	chr6:109561600-109562000	Enhancers	Right Atrium	heart

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