Variant report

Variant	rs6426937
Chromosome Location	chr1:165694918-165694919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165680183..165682740-chr1:165693137..165696252,3	K562	blood:
2	chr1:165693813..165696621-chr1:165795723..165799900,4	K562	blood:
3	chr1:165687876..165689763-chr1:165694105..165696675,2	K562	blood:
4	chr1:165684207..165686367-chr1:165693698..165695940,2	K562	blood:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10800152	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs10918266	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10918281	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12028087	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12723198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913846	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2153263	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2153264	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2790057	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2814470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3186873	0.82[ASN][1000 genomes]
rs4656462	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4657470	0.88[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6426940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656194	0.81[CHB][hapmap]
rs6670705	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679238	0.81[ASN][1000 genomes]
rs7411708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512095	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540840	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6426937	ADCY10	cis	parietal	SCAN
rs6426937	ARHGAP30	cis	parietal	SCAN
rs6426937	FCGR3A	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165685200-165695400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165685200-165696600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:165685200-165721600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:165685600-165705200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:165687000-165695200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:165687600-165695000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:165687600-165695200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:165687600-165695200	Weak transcription	NHDF-Ad	bronchial
9	chr1:165687600-165695400	Weak transcription	Osteobl	bone
10	chr1:165687600-165695600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:165687600-165695600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:165687600-165695600	Weak transcription	Fetal Thymus	thymus
13	chr1:165687600-165695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:165687600-165696200	Weak transcription	NHLF	lung
15	chr1:165687600-165696800	Weak transcription	GM12878-XiMat	blood
16	chr1:165687600-165705000	Weak transcription	Thymus	Thymus
17	chr1:165687600-165706000	Weak transcription	HepG2	liver
18	chr1:165687600-165709800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:165687600-165709800	Weak transcription	HUVEC	blood vessel
20	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:165687800-165695200	Weak transcription	Dnd41	blood
22	chr1:165687800-165695600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:165687800-165695800	Weak transcription	K562	blood
24	chr1:165687800-165696200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:165687800-165707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:165687800-165709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:165688000-165695000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:165688400-165695200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:165688800-165695400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:165688800-165695600	Weak transcription	HSMMtube	muscle
31	chr1:165689000-165695600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:165689200-165696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:165689200-165696400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:165690200-165710800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:165691000-165710000	Weak transcription	Fetal Kidney	kidney
36	chr1:165691200-165695600	Weak transcription	Primary B cells from cord blood	blood
37	chr1:165692200-165696000	Weak transcription	HMEC	breast
38	chr1:165692200-165697000	Weak transcription	Lung	lung
39	chr1:165692600-165697200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:165692800-165695000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:165693000-165695200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:165693000-165695600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:165693200-165695400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:165693200-165696000	Weak transcription	Fetal Brain Female	brain
45	chr1:165693200-165705600	Weak transcription	Ovary	ovary
46	chr1:165693400-165695200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:165693400-165695200	Weak transcription	Primary T cells from cord blood	blood
48	chr1:165693400-165695200	Weak transcription	Hela-S3	cervix
49	chr1:165693400-165695200	Weak transcription	HSMM	muscle
50	chr1:165693400-165695400	Weak transcription	Brain Hippocampus Middle	brain

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