Variant report

Variant	rs1446981
Chromosome Location	chr2:173843462-173843463
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173842376..173845001-chr2:173860642..173863497,2	MCF-7	breast:
2	chr2:173840982..173843855-chr2:173843865..173846524,2	MCF-7	breast:
3	chr2:173843217..173845112-chr2:173857829..173859868,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11687902	0.88[EUR][1000 genomes]
rs11687990	0.90[EUR][1000 genomes]
rs11885983	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs12616563	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs12624093	0.90[JPT][hapmap]
rs12693016	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs13000260	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs13413796	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1446982	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530591	0.89[CHB][hapmap]
rs16861137	0.89[CHB][hapmap]
rs16861148	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs16861173	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs17302307	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs17374295	0.90[EUR][1000 genomes]
rs1979186	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2121483	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2166588	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2242079	0.90[CHB][hapmap]
rs2258918	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2305461	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2592944	0.82[JPT][hapmap]
rs2602217	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2676521	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs3754753	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs3769228	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3769229	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3769231	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs3769233	0.88[CHB][hapmap]
rs3769236	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs3820840	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3820841	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3820842	0.89[CHB][hapmap]
rs3820843	0.90[EUR][1000 genomes]
rs3820844	0.89[EUR][1000 genomes]
rs4972393	0.89[CHB][hapmap]
rs4972523	0.90[EUR][1000 genomes]
rs66487735	0.90[EUR][1000 genomes]
rs718902	0.87[EUR][1000 genomes]
rs7603772	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1446981	HOXD8	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173832200-173850000	Weak transcription	Brain Anterior Caudate	brain
2	chr2:173832600-173850200	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:173833800-173845000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:173833800-173855600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:173833800-173859000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:173833800-173860800	Weak transcription	Right Ventricle	heart
7	chr2:173834200-173855800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:173835800-173886800	Weak transcription	Lung	lung
9	chr2:173837600-173843600	Weak transcription	Liver	Liver
10	chr2:173840400-173843600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:173841200-173843600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:173841800-173843800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:173842000-173844400	Enhancers	A549	lung
14	chr2:173842400-173850800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:173842600-173850000	Weak transcription	Fetal Heart	heart
16	chr2:173842800-173855800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:173843200-173848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:173843200-173849000	Weak transcription	Fetal Stomach	stomach
19	chr2:173843200-173850000	Weak transcription	Left Ventricle	heart
20	chr2:173843200-173850000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:173843200-173861400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:173843400-173847800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:173843400-173849400	Weak transcription	Fetal Thymus	thymus
24	chr2:173843400-173858200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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