Variant report

Variant	rs3827550
Chromosome Location	chr2:85828972-85828973
allele	C/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	POLR2A	chr2:85825703-85830272	K562	blood:	n/a	n/a
2	POLR2A	chr2:85828007-85830344	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:85825162-85830624	HepG2	liver:	n/a	n/a
4	MBD4	chr2:85828617-85829497	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:85827638-85830320	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:85825892-85830647	HepG2	liver:	n/a	n/a
7	MAX	chr2:85828624-85830757	HepG2	liver:	n/a	chr2:85829896-85829906
8	CREB1	chr2:85828748-85830704	HepG2	liver:	n/a	n/a
9	FOXA1	chr2:85828929-85829478	HepG2	liver:	n/a	n/a
10	EGR1	chr2:85828970-85829258	K562	blood:	n/a	chr2:85828983-85828993 chr2:85829128-85829141 chr2:85829131-85829141
11	HNF4G	chr2:85828831-85829839	HepG2	liver:	n/a	chr2:85829555-85829577 chr2:85829204-85829212 chr2:85829198-85829211 chr2:85829198-85829213 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829196-85829214 chr2:85829198-85829212 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829199-85829212 chr2:85829247-85829254 chr2:85829198-85829213 chr2:85829196-85829211 chr2:85829199-85829211
12	HDAC2	chr2:85828958-85830274	HepG2	liver:	n/a	chr2:85829204-85829212
13	POLR2A	chr2:85826219-85830199	HepG2	liver:	n/a	n/a
14	CHD2	chr2:85828812-85830286	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:85828266-85830248	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:85828897-85830273	A549	lung:	n/a	n/a
17	POLR2A	chr2:85825695-85830271	K562	blood:	n/a	n/a
18	POLR2A	chr2:85828339-85829949	HepG2	liver:	n/a	n/a
19	HEY1	chr2:85828646-85830566	HepG2	liver:	n/a	chr2:85829744-85829759 chr2:85829741-85829756 chr2:85829943-85829958 chr2:85829862-85829877
20	HNF4G	chr2:85828918-85829489	HepG2	liver:	n/a	chr2:85829204-85829212 chr2:85829198-85829211 chr2:85829198-85829213 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829196-85829214 chr2:85829198-85829212 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829199-85829212 chr2:85829247-85829254 chr2:85829198-85829213 chr2:85829196-85829211 chr2:85829199-85829211
21	POLR2A	chr2:85828758-85829070	Hela-S3	cervix:	n/a	n/a
22	CREB1	chr2:85828828-85830649	HepG2	liver:	n/a	n/a
23	MAX	chr2:85828924-85830542	HepG2	liver:	n/a	chr2:85829896-85829906
24	POLR2A	chr2:85828972-85830342	MCF-7	breast:	n/a	n/a
25	MYBL2	chr2:85828906-85829476	HepG2	liver:	n/a	n/a
26	RFX5	chr2:85828905-85829139	HepG2	liver:	n/a	n/a
27	NFIC	chr2:85828858-85829460	HepG2	liver:	n/a	n/a
28	HNF4A	chr2:85828883-85829457	HepG2	liver:	n/a	chr2:85829204-85829212 chr2:85829198-85829211 chr2:85829198-85829213 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829197-85829212 chr2:85829196-85829214 chr2:85829198-85829212 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829199-85829212 chr2:85829247-85829254 chr2:85829198-85829213 chr2:85829199-85829211
29	POLR2A	chr2:85825877-85830216	GM12878	blood:	n/a	n/a
30	SP1	chr2:85828946-85829482	HepG2	liver:	n/a	chr2:85829235-85829249 chr2:85829230-85829244 chr2:85829234-85829243 chr2:85829438-85829452
31	HNF4A	chr2:85828942-85829459	HepG2	liver:	n/a	chr2:85829204-85829212 chr2:85829198-85829211 chr2:85829198-85829213 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829197-85829212 chr2:85829196-85829214 chr2:85829198-85829212 chr2:85829198-85829213 chr2:85829199-85829211 chr2:85829199-85829212 chr2:85829247-85829254 chr2:85829198-85829213 chr2:85829199-85829211
32	POLR2A	chr2:85828829-85830270	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:85828393-85830576	HepG2	liver:	n/a	n/a
34	MAZ	chr2:85828860-85830564	IMR90	lung:	n/a	chr2:85829896-85829906
35	MXI1	chr2:85828773-85830871	IMR90	lung:	n/a	chr2:85829534-85829543
36	MYBL2	chr2:85828733-85830688	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:85828952-85830256	HUVEC	blood vessel:	n/a	n/a
38	TCF12	chr2:85828838-85830572	A549	lung:	n/a	n/a
39	POLR2A	chr2:85828684-85830290	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:85825324-85830119	K562	blood:	n/a	n/a
41	POLR2A	chr2:85828763-85830262	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:85828740-85830264	U87	brain:	n/a	n/a
43	MXI1	chr2:85828609-85831396	SK-N-SH	brain:	n/a	chr2:85829534-85829543 chr2:85828620-85828635
44	FOSL2	chr2:85828906-85829534	HepG2	liver:	n/a	n/a
45	PML	chr2:85828903-85830390	GM12878	blood:	n/a	n/a
46	CEBPD	chr2:85828778-85830135	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:85828807-85830264	U87	brain:	n/a	n/a
48	POLR2A	chr2:85827718-85830692	HUVEC	blood vessel:	n/a	n/a
49	MAX	chr2:85828516-85830705	HepG2	liver:	n/a	chr2:85829896-85829906

No.	Distal block	Cell Line	Cell type
1	chr2:85787126..85789513-chr2:85826931..85829549,2	K562	blood:
2	chr2:85765167..85768270-chr2:85828920..85831672,3	K562	blood:
3	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
4	chr2:85788277..85790552-chr2:85828325..85833718,7	MCF-7	breast:
5	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
6	chr2:85645470..85649377-chr2:85826700..85831557,5	MCF-7	breast:
7	chr2:85639513..85641580-chr2:85828386..85830312,2	K562	blood:
8	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
9	chr2:85646032..85649338-chr2:85826916..85831121,5	MCF-7	breast:
10	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
11	chr2:85580316..85583396-chr2:85827550..85830323,4	K562	blood:

Variant related genes	Relation type
TMEM150A	TF binding region
USP39	TF binding region
ENSG00000042493	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000042445	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10190428	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10191726	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10302	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13383605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap]
rs13418207	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14242	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1992151	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2232750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755009	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755010	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs699664	0.84[JPT][hapmap]
rs7579147	0.80[JPT][hapmap]
rs762684	0.85[JPT][hapmap]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3827550	hmm28069	cis	multi-tissue	Pritchard
rs3827550	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:85824400-85829000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:85825000-85829000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:85825800-85830400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:85826000-85829000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:85827000-85829000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:85827400-85829000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:85827600-85829000	Transcr. at gene 5' and 3'	HepG2	liver
10	chr2:85828200-85829000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:85828200-85829000	Enhancers	Esophagus	oesophagus
12	chr2:85828200-85829000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:85828200-85829200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:85828400-85829000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:85828400-85829000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:85828400-85829000	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
17	chr2:85828400-85829000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:85828400-85829000	Flanking Active TSS	HSMM	muscle
19	chr2:85828400-85829200	Enhancers	Primary B cells from cord blood	blood
20	chr2:85828400-85829200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:85828400-85829200	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr2:85828400-85829200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:85828400-85829200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr2:85828400-85829200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
25	chr2:85828400-85829400	Flanking Active TSS	Osteobl	bone
26	chr2:85828400-85829600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:85828400-85829600	Enhancers	Fetal Brain Male	brain
28	chr2:85828400-85830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:85828400-85831200	Active TSS	HSMMtube	muscle
30	chr2:85828600-85829000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:85828600-85829000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:85828600-85829000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr2:85828600-85829000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:85828600-85829000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
35	chr2:85828600-85829000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:85828600-85829000	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr2:85828600-85829000	Enhancers	Small Intestine	intestine
38	chr2:85828600-85829000	Enhancers	Stomach Mucosa	stomach
39	chr2:85828600-85829000	Enhancers	HUVEC	blood vessel
40	chr2:85828600-85829000	Flanking Active TSS	NHLF	lung
41	chr2:85828600-85829200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:85828600-85829200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:85828600-85829200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:85828600-85829200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:85828600-85829200	Enhancers	Primary T cells from cord blood	blood
46	chr2:85828600-85829200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr2:85828600-85829200	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr2:85828600-85829200	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr2:85828600-85829200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr2:85828600-85829200	Flanking Active TSS	Colon Smooth Muscle	Colon

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