Variant report

Variant	rs6676084
Chromosome Location	chr1:197094030-197094031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197090506..197092545-chr1:197093003..197095180,2	MCF-7	breast:
2	chr1:197093048..197099045-chr1:197107378..197117076,12	K562	blood:
3	chr1:197093674..197095835-chr1:197097163..197099418,3	K562	blood:
4	chr1:197092500..197094237-chr1:197110834..197113696,2	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction
ENSG00000235748	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1009188	0.84[JPT][hapmap]
rs10754210	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10754220	0.84[JPT][hapmap]
rs10922152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10922153	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap]
rs10922154	0.82[EUR][1000 genomes]
rs12140782	0.84[EUR][1000 genomes]
rs1415212	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2990510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4520444	0.81[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873069	chr1:197055925-197109042	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
4	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
5	chr1:197070600-197100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:197071000-197105400	Strong transcription	Dnd41	blood
7	chr1:197071400-197095800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:197071800-197104600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:197072600-197104600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:197072600-197107400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:197073000-197104000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:197073600-197098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
15	chr1:197074200-197102000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:197076400-197096400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:197077000-197114200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:197078200-197100400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:197080600-197105400	Strong transcription	Fetal Thymus	thymus
20	chr1:197081200-197103000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:197082000-197094600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:197083600-197098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:197083600-197108000	Strong transcription	HUVEC	blood vessel
24	chr1:197083800-197095200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:197084000-197099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:197084200-197094200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:197084200-197098400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:197084200-197098600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:197084400-197102000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:197084400-197106600	Weak transcription	Fetal Stomach	stomach
31	chr1:197084600-197100000	Strong transcription	Hela-S3	cervix
32	chr1:197085000-197095800	Strong transcription	A549	lung
33	chr1:197085800-197099800	Weak transcription	Fetal Heart	heart
34	chr1:197085800-197099800	Weak transcription	Thymus	Thymus
35	chr1:197085800-197109600	Weak transcription	Brain Germinal Matrix	brain
36	chr1:197085800-197111000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:197087600-197098600	Weak transcription	Fetal Lung	lung
38	chr1:197087800-197098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:197089200-197098600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:197089200-197105200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:197089800-197101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:197089800-197105200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:197089800-197108400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:197090000-197110800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:197090200-197098600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:197090400-197101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:197090600-197094400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:197090600-197094400	Strong transcription	NHDF-Ad	bronchial
49	chr1:197090600-197098600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:197091000-197094600	Strong transcription	NH-A	brain

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