Variant report

Variant	rs9981349
Chromosome Location	chr21:40686382-40686383
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	POLR2A	chr21:40685288-40687099	SK-N-MC	brain:	n/a	n/a
2	E2F6	chr21:40685284-40686675	H1-hESC	embryonic stem cell:	n/a	chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685550-40685560
3	POLR2A	chr21:40684951-40686864	ProgFib	skin:	n/a	n/a
4	POLR2A	chr21:40685298-40686961	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:40684903-40686876	K562	blood:	n/a	n/a
6	POLR2A	chr21:40685164-40686821	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr21:40685074-40686979	K562	blood:	n/a	n/a
8	RCOR1	chr21:40686356-40686672	K562	blood:	n/a	n/a
9	UBTF	chr21:40684951-40686805	K562	blood:	n/a	n/a
10	POLR2A	chr21:40685320-40686932	K562	blood:	n/a	n/a
11	POU2F2	chr21:40685309-40686892	GM12878	blood:	n/a	chr21:40685864-40685876 chr21:40685768-40685780 chr21:40685867-40685879
12	ETS1	chr21:40686041-40686404	K562	blood:	n/a	n/a
13	TBP	chr21:40685371-40686719	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr21:40685304-40686773	GM15510	blood:	n/a	n/a
15	E2F4	chr21:40685026-40686759	K562	blood:	n/a	chr21:40685109-40685119 chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685141-40685151 chr21:40685550-40685560 chr21:40685111-40685120
16	PML	chr21:40685283-40686737	MCF-7	breast:	n/a	n/a
17	RCOR1	chr21:40685534-40686585	GM12878	blood:	n/a	n/a
18	ZNF143	chr21:40685459-40686713	H1-hESC	embryonic stem cell:	n/a	chr21:40685866-40685884
19	RAD21	chr21:40685703-40686698	IMR90	lung:	n/a	chr21:40685853-40685867 chr21:40685855-40685868
20	CCNT2	chr21:40684902-40686697	K562	blood:	n/a	chr21:40685051-40685060 chr21:40685265-40685274 chr21:40685765-40685774
21	TCF12	chr21:40685299-40686459	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr21:40685154-40686915	HL-60	blood:	n/a	n/a
23	POLR2A	chr21:40685252-40686938	GM12891	blood:	n/a	n/a
24	SIN3AK20	chr21:40684015-40687111	MCF-7	breast:	n/a	n/a
25	POLR2A	chr21:40684347-40686942	K562	blood:	n/a	n/a
26	POLR2A	chr21:40684890-40687595	K562	blood:	n/a	n/a
27	CHD2	chr21:40685403-40686780	H1-hESC	embryonic stem cell:	n/a	chr21:40685430-40685440 chr21:40685423-40685433
28	HEY1	chr21:40684916-40686853	K562	blood:	n/a	chr21:40685861-40685876 chr21:40685748-40685763 chr21:40685144-40685159 chr21:40685469-40685484
29	MAZ	chr21:40685400-40686500	HepG2	liver:	n/a	n/a
30	POLR2A	chr21:40685056-40686987	K562	blood:	n/a	n/a
31	PAX5	chr21:40686089-40686466	GM12891	blood:	n/a	n/a
32	SMC3	chr21:40686280-40686431	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr21:40686287-40686465	HepG2	liver:	n/a	n/a
34	TBP	chr21:40685300-40686865	K562	blood:	n/a	n/a
35	MAZ	chr21:40685080-40686679	Hela-S3	cervix:	n/a	chr21:40685337-40685347 chr21:40685086-40685096
36	POLR2A	chr21:40684964-40686717	GM18526	blood:	n/a	n/a
37	REST	chr21:40683818-40686869	H1-neurons	neurons:	n/a	chr21:40685323-40685336
38	POLR2A	chr21:40685117-40686938	K562	blood:	n/a	n/a
39	SIN3A	chr21:40685536-40686469	GM12878	blood:	n/a	chr21:40685809-40685822
40	POLR2A	chr21:40685534-40686781	U87	brain:	n/a	n/a
41	TEAD4	chr21:40684911-40686578	SK-N-SH	brain:	n/a	n/a
42	CTCF	chr21:40686260-40686410	MCF-7	breast:	n/a	n/a
43	SP4	chr21:40686170-40686427	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr21:40685105-40687059	GM12892	blood:	n/a	n/a
45	ELF1	chr21:40685342-40686767	K562	blood:	n/a	chr21:40685830-40685839 chr21:40685876-40685885
46	POLR2A	chr21:40684380-40686835	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr21:40684324-40686793	GM12892	blood:	n/a	n/a
48	POLR2A	chr21:40685306-40686804	GM12878	blood:	n/a	n/a
49	POLR2A	chr21:40685286-40686822	H1-hESC	embryonic stem cell:	n/a	n/a
50	CREB1	chr21:40685239-40686659	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr2:238392237..238394703-chr21:40685639..40687456,2	MCF-7	breast:
3	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
4	chr21:40685228..40687774-chr21:40751832..40753804,3	K562	blood:
5	chr11:64545391..64546081-chr21:40685867..40686815,2	NB4	blood:
6	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
7	21:40686083-40686932..21:40748850-40752541	K562	blood:
8	21:40686083-40686932..21:40757151-40764378	K562	blood:
9	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:
10	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
11	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
12	chr21:40685837..40686745-chr5:175875260..175875880,2	Hela-S3	cervix:
13	chr20:50349937..50351852-chr21:40684525..40686487,2	MCF-7	breast:
14	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
15	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
16	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
17	chr21:40686237..40688163-chr21:40821826..40824303,2	MCF-7	breast:
18	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
19	chr21:40683489..40689074-chr21:40750757..40754639,9	MCF-7	breast:
20	chr21:40685845..40686781-chr3:9438942..9439442,2	Hela-S3	cervix:
21	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
22	chr21:40684444..40687629-chr3:63848425..63851169,6	MCF-7	breast:
23	chr21:40684138..40686385-chr9:131445458..131447217,2	MCF-7	breast:
24	chr21:40684582..40688018-chr21:40762846..40766549,4	MCF-7	breast:
25	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRWD1-IT2-1	chr21:40685861-40686888	NONHSAT082161
2	lnc-BRWD1-IT2-1	chr21:40685887-40686886	ENSG00000255568.2

Variant related genes	Relation type
BRWD1	TF binding region
BRWD1-IT2	TF binding region
BRWD1-AS1	TF binding region
ENSG00000115648	Chromatin interaction
ENSG00000113194	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000163635	Chromatin interaction
ENSG00000215444	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10154073	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12329720	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12329767	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070866	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2178838	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836941	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836946	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836947	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836962	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836963	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836970	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836976	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836978	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836979	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28397992	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28460573	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494168	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28542479	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28580194	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28590100	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665841	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28684434	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28693867	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28734946	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4818026	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7278048	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130083	0.84[EUR][1000 genomes]
rs9284464	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9305673	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs997146	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974266	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9975256	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9975728	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975909	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9975937	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976346	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9977787	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977926	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9979571	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9979691	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981527	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9982825	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9982870	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9984518	0.81[ASN][1000 genomes]
rs9984922	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985067	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9985148	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases
5	esv3439649	chr21:40683507-40687455	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	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
rs9981349	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs9981349	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40683600-40686600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr21:40683800-40686400	Active TSS	Thymus	Thymus
3	chr21:40684000-40686400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:40684000-40686400	Active TSS	Right Ventricle	heart
5	chr21:40684000-40686600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr21:40684000-40686600	Active TSS	Aorta	Aorta
7	chr21:40684000-40686600	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr21:40684200-40686400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr21:40684200-40686400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:40684200-40686400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr21:40684200-40686400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr21:40684200-40686400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr21:40684200-40686400	Active TSS	Brain Cingulate Gyrus	brain
14	chr21:40684200-40686400	Active TSS	Fetal Brain Female	brain
15	chr21:40684200-40686400	Active TSS	Pancreas	Pancrea
16	chr21:40684200-40686400	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr21:40684200-40686400	Active TSS	GM12878-XiMat	blood
18	chr21:40684200-40686600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr21:40684200-40686600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr21:40684200-40686600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:40684200-40686600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:40684200-40686600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr21:40684200-40686600	Active TSS	Fetal Intestine Large	intestine
24	chr21:40684200-40686600	Active TSS	Fetal Intestine Small	intestine
25	chr21:40684200-40686600	Active TSS	Fetal Stomach	stomach
26	chr21:40684200-40686600	Active TSS	Left Ventricle	heart
27	chr21:40684200-40686600	Active TSS	Ovary	ovary
28	chr21:40684200-40686600	Active TSS	Psoas Muscle	Psoas
29	chr21:40684200-40686600	Active TSS	Stomach Smooth Muscle	stomach
30	chr21:40684200-40686600	Active TSS	HSMM	muscle
31	chr21:40684200-40686800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr21:40684200-40686800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr21:40684400-40686400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:40684400-40686400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr21:40684400-40686400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr21:40684400-40686400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr21:40684400-40686400	Active TSS	Primary T cells from cord blood	blood
38	chr21:40684400-40686400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:40684400-40686400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr21:40684400-40686400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr21:40684400-40686400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:40684400-40686400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr21:40684400-40686400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr21:40684400-40686400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr21:40684400-40686400	Active TSS	Liver	Liver
46	chr21:40684400-40686400	Active TSS	Brain Angular Gyrus	brain
47	chr21:40684400-40686400	Active TSS	Brain Hippocampus Middle	brain
48	chr21:40684400-40686400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr21:40684400-40686400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:40684400-40686400	Active TSS	Brain Substantia Nigra	brain

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