Variant report

Variant	rs636101
Chromosome Location	chr1:120256713-120256714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120229496..120231621-chr1:120254696..120256885,2	K562	blood:
2	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
3	chr1:120188760..120191459-chr1:120254916..120257641,2	K562	blood:
4	chr1:120253275..120257099-chr1:120276679..120281090,4	K562	blood:
5	chr1:120186762..120190857-chr1:120254727..120257522,5	MCF-7	breast:
6	chr1:120255317..120256884-chr1:120262274..120265030,2	K562	blood:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10923887	0.84[EUR][1000 genomes]
rs380155	0.84[MEX][hapmap]
rs481357	0.90[JPT][hapmap]
rs541763	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs550174	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573763	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs586650	0.91[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs598100	0.95[JPT][hapmap]
rs620741	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs646124	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs663807	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667770	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs839613	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs839615	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs839616	0.92[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs636101	CD2	cis	parietal	SCAN
rs636101	PHGDH	cis	multi-tissue	Pritchard

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120254200-120256800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:120254600-120256800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:120254800-120257400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:120255400-120257000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr1:120255400-120257000	Flanking Active TSS	Liver	Liver
6	chr1:120255400-120257200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:120255400-120257200	Flanking Active TSS	Fetal Muscle Leg	muscle
8	chr1:120255600-120257000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:120255600-120257000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:120255600-120257000	Enhancers	Esophagus	oesophagus
11	chr1:120255600-120257000	Flanking Active TSS	Osteobl	bone
12	chr1:120255600-120257200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:120255600-120257200	Flanking Active TSS	Fetal Intestine Small	intestine
14	chr1:120255600-120257200	Flanking Active TSS	Fetal Lung	lung
15	chr1:120255600-120257200	Flanking Active TSS	K562	blood
16	chr1:120255600-120257400	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:120255600-120258400	Weak transcription	Right Ventricle	heart
20	chr1:120255800-120256800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:120255800-120256800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:120255800-120257000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:120255800-120257000	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:120255800-120257000	Flanking Active TSS	Fetal Kidney	kidney
25	chr1:120255800-120257000	Flanking Active TSS	Pancreas	Pancrea
26	chr1:120255800-120257000	Enhancers	Thymus	Thymus
27	chr1:120255800-120257000	Flanking Active TSS	HMEC	breast
28	chr1:120255800-120257200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:120255800-120257200	Flanking Active TSS	Fetal Intestine Large	intestine
30	chr1:120255800-120257400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr1:120255800-120257400	Transcr. at gene 5' and 3'	NHEK	skin
32	chr1:120255800-120257600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:120255800-120259400	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr1:120256000-120256800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:120256000-120256800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:120256000-120256800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:120256000-120256800	Weak transcription	Psoas Muscle	Psoas
38	chr1:120256000-120257000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr1:120256000-120257200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr1:120256000-120257400	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
41	chr1:120256000-120257600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:120256000-120257600	Enhancers	Placenta	Placenta
43	chr1:120256000-120258800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:120256000-120258800	Enhancers	Ovary	ovary
45	chr1:120256000-120259000	Enhancers	Adipose Nuclei	Adipose
46	chr1:120256000-120259400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
47	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr1:120256200-120256800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:120256200-120256800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:120256200-120257000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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