Variant report

Variant	rs544115
Chromosome Location	chr11:74705696-74705697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74704735..74707299-chr11:74968333..74971046,2	K562	blood:
2	chr11:74698148..74702654-chr11:74704592..74707989,9	K562	blood:
3	chr11:74705536..74708184-chr11:74711771..74713788,3	K562	blood:
4	chr11:74704465..74706580-chr11:74709652..74711304,2	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11236291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827626	0.80[CEU][hapmap]
rs12287793	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866562	0.80[CEU][hapmap]
rs3018833	0.89[ASN][1000 genomes]
rs483271	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs487226	0.81[JPT][hapmap]
rs493001	0.81[JPT][hapmap]
rs494474	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4944962	0.81[JPT][hapmap]
rs500827	0.81[JPT][hapmap]
rs503855	0.80[CEU][hapmap]
rs512782	0.81[JPT][hapmap]
rs514534	0.81[JPT][hapmap]
rs517666	0.81[JPT][hapmap]
rs522808	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544891	0.81[JPT][hapmap]
rs551371	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565377	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs566480	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568310	0.91[ASN][1000 genomes]
rs578477	0.81[JPT][hapmap]
rs579581	0.81[JPT][hapmap]
rs58778107	0.96[ASN][1000 genomes]
rs58972415	0.85[ASN][1000 genomes]
rs59860682	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605954	0.81[JPT][hapmap]
rs629191	0.81[JPT][hapmap]
rs639768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650130	0.81[JPT][hapmap]
rs662062	0.81[JPT][hapmap]
rs670246	0.81[JPT][hapmap]
rs671544	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs673731	0.80[CEU][hapmap]
rs674122	0.93[ASN][1000 genomes]
rs681566	0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs685116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693212	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs7128833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939123	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952096	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952209	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.87[EUR][1000 genomes];0.97[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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs544115	PAAF1	cis	cerebellum	SCAN
rs544115	XRRA1	cis	lymphoblastoid	seeQTL
rs544115	XRRA1	cis	parietal	SCAN
rs544115	KCTD21	cis	cerebellum	SCAN
rs544115	IL18BP	cis	cerebellum	SCAN
rs544115	FCHSD2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74700400-74716400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74700400-74723000	Weak transcription	Small Intestine	intestine
3	chr11:74700600-74716400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:74700600-74716400	Weak transcription	Aorta	Aorta
5	chr11:74700600-74716400	Weak transcription	Esophagus	oesophagus
6	chr11:74700600-74716400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:74700600-74716600	Weak transcription	Fetal Brain Male	brain
8	chr11:74700600-74722600	Weak transcription	HSMM	muscle
9	chr11:74700600-74725000	Weak transcription	HSMMtube	muscle
10	chr11:74700800-74705800	Weak transcription	Placenta	Placenta
11	chr11:74700800-74716400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:74700800-74716400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:74700800-74716400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:74700800-74716400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:74700800-74716400	Weak transcription	NHLF	lung
16	chr11:74700800-74716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:74701000-74705800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:74701000-74705800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:74701000-74705800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:74701000-74705800	Weak transcription	Fetal Lung	lung
21	chr11:74701000-74705800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:74701000-74705800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:74701000-74705800	Weak transcription	NHDF-Ad	bronchial
24	chr11:74701000-74707600	Weak transcription	Right Atrium	heart
25	chr11:74701000-74716400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:74701000-74716400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:74701000-74716400	Weak transcription	Colonic Mucosa	Colon
28	chr11:74701000-74716600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:74701000-74716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:74701000-74716600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:74701000-74716600	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:74701000-74716600	Weak transcription	NH-A	brain
33	chr11:74701000-74722000	Weak transcription	Fetal Kidney	kidney
34	chr11:74701000-74722600	Weak transcription	HUVEC	blood vessel
35	chr11:74701000-74723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:74701200-74716400	Weak transcription	A549	lung
37	chr11:74701400-74716400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:74701600-74721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:74701800-74716600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:74702400-74716600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:74702400-74716600	Weak transcription	Fetal Heart	heart
42	chr11:74702400-74722800	Weak transcription	Stomach Mucosa	stomach
43	chr11:74702800-74716400	Weak transcription	Pancreas	Pancrea
44	chr11:74702800-74717600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr11:74703200-74705800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:74703200-74707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:74703200-74720600	Weak transcription	Psoas Muscle	Psoas
48	chr11:74704400-74708400	Strong transcription	Fetal Thymus	thymus
49	chr11:74704600-74706400	Strong transcription	Hela-S3	cervix
50	chr11:74704600-74707200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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