Variant report

Variant	rs1891000
Chromosome Location	chr1:225689665-225689666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225689503..225693745-chr1:225697165..225700935,4	K562	blood:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10495242	0.93[YRI][hapmap]
rs10799312	0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs10799320	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915831	0.80[ASN][1000 genomes]
rs10915836	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11588279	0.83[CHB][hapmap]
rs12032961	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs12034829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340865	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs1764347	0.82[AMR][1000 genomes]
rs1771316	1.00[YRI][hapmap]
rs1771318	0.82[AMR][1000 genomes]
rs2039620	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2066233	0.83[CHB][hapmap]
rs2185528	0.80[ASN][1000 genomes]
rs3766930	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs3893032	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs4233220	0.84[ASN][1000 genomes]
rs4554690	0.90[ASN][1000 genomes]
rs4653638	0.87[JPT][hapmap]
rs481746	0.82[AMR][1000 genomes]
rs499782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426075	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6692054	0.84[ASN][1000 genomes]
rs6696038	0.83[CHB][hapmap]
rs6702641	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522622	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527014	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527184	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7529690	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426126	0.87[ASN][1000 genomes]
rs954534	0.82[AMR][1000 genomes]
rs9725758	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1891000	C1orf95	cis	cerebellum	SCAN
rs1891000	HHIPL2	cis	cerebellum	SCAN
rs1891000	DUSP10	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:225666000-225696800	Weak transcription	Esophagus	oesophagus
3	chr1:225669800-225696800	Weak transcription	Pancreas	Pancrea
4	chr1:225672200-225696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225672200-225696800	Weak transcription	Brain Germinal Matrix	brain
6	chr1:225672800-225693800	Weak transcription	Left Ventricle	heart
7	chr1:225673600-225693800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:225674400-225696800	Weak transcription	Aorta	Aorta
9	chr1:225674800-225693800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:225676200-225696400	Weak transcription	Gastric	stomach
11	chr1:225677200-225696000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:225677200-225696400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:225677200-225696400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:225677200-225696400	Weak transcription	Brain Substantia Nigra	brain
15	chr1:225677200-225696400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:225677200-225696600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:225677200-225696600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:225677200-225696600	Weak transcription	Psoas Muscle	Psoas
19	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
20	chr1:225679600-225696000	Weak transcription	Hela-S3	cervix
21	chr1:225680000-225690600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:225680200-225695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:225680200-225696200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:225680800-225691000	Strong transcription	NH-A	brain
25	chr1:225680800-225696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:225681200-225696200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:225681800-225699800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:225683000-225696000	Weak transcription	HMEC	breast
29	chr1:225683000-225696800	Weak transcription	Lung	lung
30	chr1:225683200-225693800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:225683400-225693800	Weak transcription	Liver	Liver
32	chr1:225683400-225696600	Weak transcription	Right Ventricle	heart
33	chr1:225684200-225696800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:225685400-225693600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225685600-225694200	Weak transcription	Fetal Brain Male	brain
36	chr1:225686200-225692600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:225686400-225693800	Weak transcription	Fetal Kidney	kidney
38	chr1:225686400-225693800	Weak transcription	HepG2	liver
39	chr1:225686600-225695800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:225686800-225690200	Strong transcription	Fetal Lung	lung
41	chr1:225686800-225693800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:225686800-225693800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:225686800-225693800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:225686800-225695800	Weak transcription	HUVEC	blood vessel
45	chr1:225686800-225695800	Weak transcription	NHLF	lung
46	chr1:225686800-225696200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:225686800-225696400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:225686800-225696400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:225686800-225696400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:225686800-225699800	Weak transcription	Adipose Nuclei	Adipose

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