Variant report

Variant	rs2550868
Chromosome Location	chr16:72066072-72066073
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	chr16:72063644..72068300-chr16:72070682..72074254,4	K562	blood:
2	chr16:72044548..72046611-chr16:72064747..72066646,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10048111	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10048144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10400963	0.85[JPT][hapmap]
rs10492813	0.86[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap]
rs10492814	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs1050361	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1050363	0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs10852511	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11075924	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs11643192	0.80[JPT][hapmap]
rs12162087	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12325266	0.80[JPT][hapmap]
rs12443622	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12446480	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12449073	0.85[JPT][hapmap]
rs12917999	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12924413	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12930205	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12930702	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12932845	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs16973716	0.90[JPT][hapmap];0.88[YRI][hapmap]
rs2070937	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2070939	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2072141	0.86[CHB][hapmap]
rs2081222	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2081223	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236765	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2241411	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2287998	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287999	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288000	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288001	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288002	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303285	0.82[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap]
rs251033	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550035	0.86[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2550038	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2550869	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2550870	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2550876	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2854956	0.83[YRI][hapmap]
rs2878404	0.83[CHD][hapmap]
rs3764310	0.83[CHD][hapmap]
rs3764311	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs3764314	0.86[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap]
rs3812984	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3812986	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3844425	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs3852781	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs3852782	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3852784	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs3890860	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3909541	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4238964	0.85[JPT][hapmap]
rs4788458	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4788598	0.96[YRI][hapmap]
rs4788609	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4788610	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs56139130	0.87[ASN][1000 genomes]
rs6499557	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6499562	0.90[JPT][hapmap]
rs7185840	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7188962	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7189115	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7189591	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7190994	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7192848	0.80[JPT][hapmap]
rs7199261	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7200854	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7201225	0.80[JPT][hapmap]
rs7201643	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7201866	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7202268	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7203426	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7203821	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7350838	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs8044868	0.90[JPT][hapmap]
rs8050238	0.84[YRI][hapmap]
rs8052338	0.85[JPT][hapmap]
rs8052408	0.90[JPT][hapmap]
rs8053907	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8059437	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs8062895	0.83[CHD][hapmap]
rs8182213	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9924964	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9926927	0.86[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap]
rs9927526	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9928157	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9930890	0.82[ASN][1000 genomes]
rs9932951	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9936642	0.80[JPT][hapmap]
rs9938382	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2550868	DHX38	cis	lymphoblastoid	seeQTL
rs2550868	NRN1L	cis	parietal	SCAN
rs2550868	HP	cis	parietal	SCAN
rs2550868	HPR	cis	parietal	SCAN
rs2550868	HP	cis	cerebellum	SCAN
rs2550868	DHODH	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043200-72069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:72043200-72069800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:72043600-72075200	Weak transcription	Fetal Brain Male	brain
4	chr16:72051400-72078600	Weak transcription	Fetal Kidney	kidney
5	chr16:72058200-72069800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:72058200-72072200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr16:72058200-72076000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:72058200-72076000	Weak transcription	HSMMtube	muscle
9	chr16:72058200-72077000	Weak transcription	Colonic Mucosa	Colon
10	chr16:72058200-72078000	Weak transcription	Fetal Lung	lung
11	chr16:72058600-72069800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:72059400-72069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr16:72059600-72084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:72059800-72069200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr16:72060000-72073200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:72060000-72079200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr16:72060200-72069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:72060200-72070000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr16:72060200-72075600	Weak transcription	Lung	lung
20	chr16:72060200-72075600	Weak transcription	Pancreas	Pancrea
21	chr16:72060200-72075800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:72060200-72075800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr16:72060200-72076200	Weak transcription	Brain Angular Gyrus	brain
24	chr16:72060200-72076200	Weak transcription	Placenta	Placenta
25	chr16:72060200-72076400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr16:72060200-72080000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
29	chr16:72060400-72068600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr16:72060600-72075800	Weak transcription	Brain Germinal Matrix	brain
31	chr16:72061600-72068000	Weak transcription	Fetal Intestine Large	intestine
32	chr16:72061600-72069800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr16:72061600-72075200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:72061600-72075800	Weak transcription	Brain Anterior Caudate	brain
35	chr16:72061600-72076200	Weak transcription	Fetal Intestine Small	intestine
36	chr16:72062000-72072000	Weak transcription	Ovary	ovary
37	chr16:72062000-72076000	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:72062000-72076000	Weak transcription	Thymus	Thymus
39	chr16:72062200-72069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:72062200-72075400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr16:72062200-72075600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:72062200-72079600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:72062200-72080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:72062400-72066600	Weak transcription	Dnd41	blood
45	chr16:72062400-72075400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr16:72062400-72075800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr16:72062400-72075800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr16:72062400-72076000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr16:72062400-72076000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr16:72062400-72076000	Weak transcription	Spleen	Spleen

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