Variant report

Variant	rs6542180
Chromosome Location	chr2:114653871-114653872
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
2	chr2:114651373..114654113-chr2:114668115..114670436,3	K562	blood:
3	chr2:114512332..114515034-chr2:114651411..114654635,3	MCF-7	breast:
4	chr2:114653670..114656368-chr2:114668759..114670499,2	MCF-7	breast:
5	chr2:114645610..114649008-chr2:114652847..114656238,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270019	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1028245	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11123214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11675908	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11684182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685296	0.84[ASN][1000 genomes]
rs11685654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691664	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1403401	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17197632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35167892	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4241126	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4571059	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849285	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849286	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849287	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849288	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849289	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs4849290	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs4849291	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4849294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849296	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57106417	0.81[ASN][1000 genomes]
rs61050591	0.84[ASN][1000 genomes]
rs62169889	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169929	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169935	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62171760	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62171761	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62171768	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62171769	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72835479	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576537	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579001	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605071	0.83[CHB][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6542180	DDX11L2	cis	Whole Blood	GTEx
rs6542180	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs6542180	RPL23AP7	cis	Whole Blood	GTEx
rs6542180	SLC35F5	cis	Thyroid	GTEx
rs6542180	DDX11L2	cis	lung	GTEx
rs6542180	RPL23AP7	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114648600-114657800	Weak transcription	Gastric	stomach
2	chr2:114648600-114667600	Weak transcription	Lung	lung
3	chr2:114649200-114661200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:114649200-114673200	Weak transcription	Placenta	Placenta
5	chr2:114649400-114654000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr2:114649400-114655200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:114649600-114661000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:114649800-114655600	Enhancers	Small Intestine	intestine
9	chr2:114650000-114654400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:114650000-114655600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:114650200-114654200	Genic enhancers	HSMM	muscle
12	chr2:114650200-114654600	Genic enhancers	Dnd41	blood
13	chr2:114650200-114658400	Enhancers	Adipose Nuclei	Adipose
14	chr2:114650200-114658400	Enhancers	Stomach Mucosa	stomach
15	chr2:114650200-114661000	Weak transcription	Right Ventricle	heart
16	chr2:114650400-114654400	Weak transcription	Fetal Lung	lung
17	chr2:114650400-114655400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:114650600-114654200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:114651200-114654200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:114651200-114655800	Enhancers	Brain Hippocampus Middle	brain
21	chr2:114651400-114654000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:114651400-114654600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr2:114651600-114658000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:114652000-114654200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:114652000-114654400	Enhancers	Thymus	Thymus
26	chr2:114652000-114656000	Enhancers	NHLF	lung
27	chr2:114652000-114658000	Weak transcription	Pancreas	Pancrea
28	chr2:114652000-114667600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:114652000-114667600	Weak transcription	Esophagus	oesophagus
30	chr2:114652200-114654000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:114652200-114654000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:114652200-114654000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:114652200-114654200	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr2:114652200-114654600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:114652200-114658000	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:114652200-114700600	Weak transcription	Fetal Brain Male	brain
37	chr2:114652400-114654000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:114652400-114654000	Weak transcription	HSMMtube	muscle
39	chr2:114652400-114654200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:114652400-114654200	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:114652400-114654600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:114652400-114654600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:114652400-114655200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:114652400-114655400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr2:114652400-114655400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr2:114652400-114655400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:114652400-114655800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:114652400-114656400	Weak transcription	Brain Germinal Matrix	brain
49	chr2:114652400-114656800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:114652400-114657200	Enhancers	HUVEC	blood vessel

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