Variant report

Variant	rs10191938
Chromosome Location	chr2:48627956-48627957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10182093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10195717	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10197359	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11674217	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11674317	0.80[CEU][hapmap]
rs11676078	0.92[EUR][1000 genomes]
rs11677205	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11678934	0.88[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs11679685	0.83[EUR][1000 genomes]
rs11682838	0.87[EUR][1000 genomes]
rs11683202	1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11687461	1.00[CEU][hapmap]
rs11687771	0.82[CEU][hapmap]
rs11689285	0.88[CEU][hapmap]
rs11690526	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs11691302	0.91[EUR][1000 genomes]
rs11691407	0.91[EUR][1000 genomes]
rs11692537	0.88[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11694094	0.89[EUR][1000 genomes]
rs11694955	0.82[EUR][1000 genomes]
rs13394813	0.87[AFR][1000 genomes]
rs13398456	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17397449	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs28505584	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2937	0.88[CEU][hapmap]
rs4364065	0.83[EUR][1000 genomes]
rs4438532	0.81[YRI][hapmap]
rs4606978	0.81[YRI][hapmap]
rs6747738	0.88[CEU][hapmap]
rs72889641	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7573281	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7584796	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs952468	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10191938	KLRAQ1	cis	parietal	SCAN
rs10191938	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48625800-48628600	Enhancers	Brain Angular Gyrus	brain
2	chr2:48626000-48628000	Enhancers	Brain Hippocampus Middle	brain
3	chr2:48626000-48628400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48626200-48628000	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:48626400-48628000	Weak transcription	Fetal Brain Female	brain
6	chr2:48626400-48628400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:48626400-48628400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:48626400-48628400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:48626600-48628000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:48626600-48628200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:48626800-48628200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr2:48626800-48628200	Enhancers	Fetal Intestine Small	intestine
13	chr2:48626800-48628600	Enhancers	Duodenum Mucosa	Duodenum
14	chr2:48627000-48628000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:48627400-48632200	Weak transcription	Fetal Intestine Large	intestine
16	chr2:48627800-48628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:48627800-48628200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:48627800-48628200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:48627800-48628400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr2:48627800-48628400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:48627800-48628800	Enhancers	Brain Substantia Nigra	brain

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