Variant report

Variant	rs544404
Chromosome Location	chr1:225770798-225770799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225770172..225772127-chr1:225789997..225792684,2	K562	blood:
2	chr1:225762925..225765208-chr1:225770606..225772891,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10082003	0.83[AMR][1000 genomes]
rs10915853	0.85[AMR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1222439	0.88[EUR][1000 genomes]
rs1336480	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360958	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629896	0.88[TSI][hapmap]
rs1764345	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771318	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035916	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3904084	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs475794	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481746	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516323	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526221	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59363938	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426075	0.89[TSI][hapmap]
rs72750896	0.82[EUR][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9651009	0.90[AMR][1000 genomes];0.91[EUR][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	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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs544404	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
2	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
3	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:225755200-225772200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:225766400-225780000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:225766400-225783600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:225766600-225779600	Weak transcription	NH-A	brain
11	chr1:225767000-225773600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:225767600-225770800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:225768400-225781200	Weak transcription	Right Ventricle	heart
14	chr1:225768600-225787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:225768800-225781000	Weak transcription	HSMM	muscle
16	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
17	chr1:225769000-225774400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:225769000-225783000	Weak transcription	HSMMtube	muscle
19	chr1:225769200-225773600	Weak transcription	Fetal Stomach	stomach
20	chr1:225769200-225773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:225769200-225775000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:225769200-225779800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:225769200-225783200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:225769400-225779600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:225769800-225770800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:225769800-225770800	Strong transcription	Osteobl	bone
27	chr1:225769800-225771000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:225769800-225772000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:225770000-225773600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:225770000-225773600	Weak transcription	Lung	lung
31	chr1:225770000-225780000	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:225770000-225782000	Weak transcription	Right Atrium	heart
33	chr1:225770000-225783200	Weak transcription	Psoas Muscle	Psoas
34	chr1:225770000-225785200	Weak transcription	Left Ventricle	heart
35	chr1:225770000-225787600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:225770200-225779600	Weak transcription	Fetal Lung	lung
37	chr1:225770400-225771800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:225770400-225772600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:225770400-225773800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:225770400-225778200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:225770400-225780000	Weak transcription	Ovary	ovary
42	chr1:225770600-225770800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:225770600-225771000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:225770600-225774000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:225770600-225774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:225770600-225775200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:225770600-225776200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:225770600-225776600	Weak transcription	A549	lung
49	chr1:225770600-225777800	Weak transcription	Fetal Heart	heart
50	chr1:225770600-225778200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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