Variant report

Variant	rs2227909
Chromosome Location	chr19:36370011-36370012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr19:36369932-36370397	K562	blood:	n/a	chr19:36370200-36370211 chr19:36370194-36370216 chr19:36370199-36370212 chr19:36370199-36370209 chr19:36370200-36370210 chr19:36370199-36370212 chr19:36370165-36370178 chr19:36370198-36370213 chr19:36370199-36370212 chr19:36370198-36370212 chr19:36370199-36370212 chr19:36370200-36370210 chr19:36370200-36370209
2	EGR1	chr19:36369997-36370347	K562	blood:	n/a	chr19:36370200-36370211 chr19:36370194-36370216 chr19:36370199-36370212 chr19:36370199-36370209 chr19:36370200-36370210 chr19:36370199-36370212 chr19:36370165-36370178 chr19:36370198-36370213 chr19:36370199-36370212 chr19:36370198-36370212 chr19:36370199-36370212 chr19:36370200-36370210 chr19:36370200-36370209
3	CTCF	chr19:36369980-36370130	GM12868	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36365053..36367604-chr19:36368904..36371843,2	MCF-7	breast:
2	chr19:36359256..36363302-chr19:36368429..36371554,3	K562	blood:
3	chr19:36363822..36367543-chr19:36368056..36371316,4	K562	blood:
4	chr19:36359233..36364587-chr19:36367940..36372688,7	K562	blood:

Variant related genes	Relation type
RN7SL402P	TF binding region
APLP1	TF binding region
ENSG00000105290	Chromatin interaction
ENSG00000161270	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11084834	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880785	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs11880909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881358	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11881364	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970737	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16970742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549166	0.83[ASN][1000 genomes]
rs2228998	0.91[ASN][1000 genomes]
rs230260	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs230261	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs230262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230265	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230268	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs230269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871778	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34006827	1.00[EUR][1000 genomes]
rs35423326	1.00[EUR][1000 genomes]
rs376240	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs392702	0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs393116	1.00[EUR][1000 genomes]
rs401824	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs404299	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs412175	0.87[EUR][1000 genomes]
rs417786	0.86[EUR][1000 genomes]
rs437168	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs443186	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs447783	0.86[EUR][1000 genomes]
rs4806227	0.87[ASN][1000 genomes]
rs55797913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55816190	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264349	0.91[EUR][1000 genomes]
rs57002105	0.81[ASN][1000 genomes]
rs57053076	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57113091	0.87[ASN][1000 genomes]
rs57668132	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57911093	0.91[ASN][1000 genomes]
rs58098901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58109577	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58291714	0.95[EUR][1000 genomes]
rs58504183	0.81[EUR][1000 genomes]
rs58551711	0.81[EUR][1000 genomes]
rs59123406	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59658571	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60268250	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576074	0.95[EUR][1000 genomes]
rs60869994	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60935148	0.81[EUR][1000 genomes]
rs61623584	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619833	1.00[EUR][1000 genomes]
rs7251744	1.00[EUR][1000 genomes]
rs7251879	0.85[TSI][hapmap]
rs7253086	0.81[EUR][1000 genomes]
rs7256433	0.81[EUR][1000 genomes]
rs7258909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73590883	0.85[EUR][1000 genomes]
rs73594463	0.81[EUR][1000 genomes]
rs73599600	0.81[EUR][1000 genomes]
rs73928331	0.90[EUR][1000 genomes]
rs73928332	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73928333	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807660	1.00[EUR][1000 genomes]
rs8106732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110926	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111209	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111348	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879407	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9749325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	esv3397651	chr19:36326933-36377725	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36359800-36370200	Weak transcription	HSMMtube	muscle
2	chr19:36360200-36379000	Weak transcription	Aorta	Aorta
3	chr19:36361000-36389000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:36361200-36370400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:36361200-36370400	Weak transcription	NH-A	brain
6	chr19:36361200-36389200	Weak transcription	Right Atrium	heart
7	chr19:36361400-36370200	Strong transcription	Brain Anterior Caudate	brain
8	chr19:36361400-36370200	Weak transcription	A549	lung
9	chr19:36361800-36370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:36361800-36370400	Strong transcription	Fetal Brain Female	brain
11	chr19:36362000-36370200	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr19:36362000-36370400	Strong transcription	Brain Germinal Matrix	brain
13	chr19:36362000-36373200	Weak transcription	Fetal Brain Male	brain
14	chr19:36362200-36370400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:36362400-36378200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:36362600-36378000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:36364800-36370800	Weak transcription	Esophagus	oesophagus
18	chr19:36366000-36378200	Weak transcription	Gastric	stomach
19	chr19:36367200-36371200	Genic enhancers	Brain Hippocampus Middle	brain
20	chr19:36367800-36378400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:36368600-36370600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:36369000-36370400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:36369600-36371000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:36369800-36370400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr19:36369800-36370400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:36369800-36370600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:36369800-36370800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr19:36369800-36371200	Enhancers	Brain Substantia Nigra	brain
29	chr19:36369800-36372800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:36370000-36370200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:36370000-36370200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:36370000-36370200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr19:36370000-36370200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr19:36370000-36370200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:36370000-36370400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:36370000-36370800	Enhancers	Brain Cingulate Gyrus	brain
37	chr19:36370000-36371000	Enhancers	Pancreas	Pancrea
38	chr19:36370000-36371200	Enhancers	K562	blood
39	chr19:36370000-36373200	Weak transcription	Brain Angular Gyrus	brain

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